5ZF0

X-ray Structure of the Electron Transfer Complex between Ferredoxin and Photosystem I

• PDB DOI: https://doi.org/10.2210/pdb5ZF0/pdb

• Classification: PHOTOSYNTHESIS/ELECTRON TRANSPORT
• Organism(s): Thermosynechococcus vestitus BP-1, Thermosynechococcus vestitus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2018-03-01 Released: 2018-04-11 
• Deposition Author(s): Kubota-Kawai, H., Mutoh, R., Shinmura, K., Setif, P., Nowaczyk, M., Roegner, M., Ikegami, T., Tanaka, T., Kurisu, G.
• Funding Organization(s): Japan Society for the Promotion of Science, Japan science and technology agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free: 
  0.377 (Depositor), 0.380 (DCC) 
• R-Value Work: 
  0.353 (Depositor), 0.360 (DCC) 
• R-Value Observed: 
  0.354 (Depositor) 

Starting Model: experimental

Literature

X-ray structure of an asymmetrical trimeric ferredoxin-photosystem I complex

Kubota-Kawai, H., Mutoh, R., Shinmura, K., Setif, P., Nowaczyk, M.M., Rogner, M., Ikegami, T., Tanaka, H., Kurisu, G.

(2018) Nat Plants 4: 218-224

• PubMed: 29610537 
• DOI: https://doi.org/10.1038/s41477-018-0130-0
• Primary Citation of Related Structures:  
  5ZF0


• PubMed Abstract: 
  

  Photosystem I (PSI), a large protein complex located in the thylakoid membrane, mediates the final step in light-driven electron transfer to the stromal electron carrier protein ferredoxin (Fd). Here, we report the first structural description of the PSI-Fd complex from Thermosynechococcus elongatus. The trimeric PSI complex binds three Fds in a non-equivalent manner. While each is recognized by a PSI protomer in a similar orientation, the distances between Fds and the PSI redox centres differ. Fd binding thus entails loss of the exact three-fold symmetry of the PSI's soluble subunits, inducing structural perturbations which are transferred to the lumen through PsaF. Affinity chromatography and nuclear magnetic resonance analyses of PSI-Fd complexes support the existence of two different Fd-binding states, with one Fd being more tightly bound than the others. We propose a dynamic structural basis for productive complex formation, which supports fast electron transfer between PSI and Fd.

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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Osaka, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 39-mer - A3B3C3D3E3F3G3H3I3J3K3L3M3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 39-mer - A6B6C3D3E3F3G3H3I3J3K3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 39-mer - A3B3C3D3E3F3G3H3I3J3K3L3M3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 39-mer - A6B5C4D3E3F3G3H3I3J3K3 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2,223.59 kDa 
• Atom Count: 148,494 
• Modelled Residue Count: 14,040 
• Deposited Residue Count: 14,586 
• Unique protein chains: 13

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A [auth A1], IB [auth A5], KA [auth A4], M [auth A2], WA [auth A6], Y [auth A3]	755	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P0A405 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A405  Go to UniProtKB:  P0A405

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B [auth B1], JB [auth B5], LA [auth B4], N [auth B2], XA [auth B6], Z [auth B3]	740	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P0A407 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A407  Go to UniProtKB:  P0A407

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	AA [auth C3], C [auth C1], KB [auth C5], MA [auth C4], O [auth C2], YA [auth C6]	80	Thermosynechococcus vestitus BP-1	Mutation(s): 0  EC: 1.97.1.12 Membrane Entity: Yes
UniProt
Find proteins for P0A415 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A415  Go to UniProtKB:  P0A415

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit II	BA [auth D3], D [auth D1], LB [auth D5], NA [auth D4], P [auth D2], ZA [auth D6]	138	Thermosynechococcus vestitus BP-1	Mutation(s): 0
UniProt
Find proteins for P0A420 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A420  Go to UniProtKB:  P0A420

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	AB [auth E6], CA [auth E3], E [auth E1], MB [auth E5], OA [auth E4], Q [auth E2]	75	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A423 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A423  Go to UniProtKB:  P0A423

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit III	BB [auth F6], DA [auth F3], F [auth F1], NB [auth F5], PA [auth F4], R [auth F2]	164	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A401 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A401  Go to UniProtKB:  P0A401

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit VIII	CB [auth I6], EA [auth I3], G [auth I1], OB [auth I5], QA [auth I4], S [auth I2]	38	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A427 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A427  Go to UniProtKB:  P0A427

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	DB [auth J6], FA [auth J3], H [auth J1], PB [auth J5], RA [auth J4], T [auth J2]	41	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A429 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A429  Go to UniProtKB:  P0A429

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK	EB [auth K6], GA [auth K3], I [auth K1], QB [auth K5], SA [auth K4], U [auth K2]	83	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A425 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A425  Go to UniProtKB:  P0A425

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XI	FB [auth L6], HA [auth L3], J [auth L1], RB [auth L5], TA [auth L4], V [auth L2]	154	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q8DGB4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DGB4  Go to UniProtKB:  Q8DGB4

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit XII	GB [auth M6], IA [auth M3], K [auth M1], SB [auth M5], UA [auth M4], W [auth M2]	31	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P0A403 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A403  Go to UniProtKB:  P0A403

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
PsaX	HB [auth X6], JA [auth X3], L [auth X1], TB [auth X5], VA [auth X4], X [auth X2]	35	Thermosynechococcus vestitus	Mutation(s): 0

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferredoxin-1	UB [auth P1], VB [auth P2], WB [auth P3], XB [auth P4], YB [auth P6], ZB [auth P5]	97	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Gene Names: petF1, petF, tsl1009
UniProt
Find proteins for P0A3C9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore P0A3C9  Go to UniProtKB:  P0A3C9

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLA	AAA [auth J6], ABA [auth A5], AC [auth A1], ACA [auth A5], AD [auth A1], ADA [auth B5], AE [auth B1], AEA [auth B5], AF [auth B1], AH [auth A2], AI [auth A2], AK [auth B2], AM [auth A3], AN [auth A3], AO [auth B3], AP [auth B3], AR [auth A4], AS [auth A4], AT [auth B4], AU [auth B4], AW [auth A6], AX [auth A6], AY [auth B6], AZ [auth B6], BBA [auth A5], BC [auth A1], BCA [auth A5], BD [auth A1], BDA [auth B5], BE [auth B1], BEA [auth B5], BF [auth B1], BH [auth A2], BI [auth A2], BJ [auth B2], BK [auth B2], BM [auth A3], BN [auth A3], BO [auth B3], BP [auth B3], BQ [auth F3], BR [auth A4], BS [auth A4], BT [auth B4], BU [auth B4], BW [auth A6], BX [auth A6], BY [auth B6], BZ [auth B6], CBA [auth A5], CC [auth A1], CCA [auth A5], CD [auth A1], CDA [auth B5], CE [auth B1], CEA [auth B5], CF [auth B1], CFA [auth K5], CG [auth F1], CH [auth A2], CI [auth A2], CJ [auth B2], CK [auth B2], CL [auth F2], CM [auth A3], CN [auth A3], CO [auth B3], CP [auth B3], CR [auth A4], CS [auth A4], CT [auth B4], CU [auth B4], CW [auth A6], CX [auth A6], CY [auth B6], CZ [auth B6], DAA [auth K6], DBA [auth A5], DC [auth A1], DCA [auth A5], DD [auth A1], DDA [auth B5], DE [auth B1], DEA [auth B5], DF [auth B1], DFA [auth K5], DH [auth A2], DI [auth A2], DJ [auth B2], DK [auth B2], DM [auth A3], DN [auth A3], DO [auth B3], DP [auth B3], DR [auth A4], DS [auth A4], DT [auth B4], DU [auth B4], DV [auth J4], DW [auth A6], DX [auth A6], DY [auth B6], DZ [auth B6], EBA [auth A5], EC [auth A1], ECA [auth A5], ED [auth A1], EDA [auth B5], EE [auth B1], EEA [auth B5], EF [auth B1], EG [auth I1], EH [auth A2], EI [auth A2], EJ [auth B2], EK [auth B2], EL [auth F2], EM [auth A3], EN [auth A3], EO [auth B3], EP [auth B3], ER [auth A4], ES [auth A4], ET [auth B4], EU [auth B4], EV [auth J4], EW [auth A6], EX [auth A6], EY [auth B6], EZ [auth B6], FAA [auth L6], FBA [auth A5], FC [auth A1], FCA [auth A5], FD [auth A1], FDA [auth B5], FE [auth B1], FEA [auth B5], FF [auth B1], FFA [auth L5], FH [auth A2], FI [auth A2], FJ [auth B2], FK [auth B2], FM [auth A3], FN [auth A3], FO [auth B3], FP [auth B3], FQ [auth J3], FR [auth A4], FS [auth A4], FT [auth B4], FU [auth B4], FW [auth A6], FX [auth A6], FY [auth B6], FZ [auth B6], GAA [auth L6], GBA [auth A5], GC [auth A1], GCA [auth A5], GD [auth A1], GDA [auth B5], GE [auth B1], GEA [auth B5], GF [auth B1], GFA [auth L5], GH [auth A2], GI [auth A2], GJ [auth B2], GK [auth B2], GL [auth J2], GM [auth A3], GN [auth A3], GO [auth B3], GP [auth B3], GQ [auth J3], GR [auth A4], GS [auth A4], GT [auth B4], GU [auth B4], GW [auth A6], GX [auth A6], GY [auth B6], GZ [auth B6], HBA [auth A5], HC [auth A1], HD [auth A1], HDA [auth B5], HE [auth B1], HEA [auth B5], HF [auth B1], HFA [auth L5], HG [auth J1], HH [auth A2], HI [auth A2], HJ [auth B2], HK [auth B2], HM [auth A3], HN [auth A3], HO [auth B3], HP [auth B3], HR [auth A4], HS [auth A4], HT [auth B4], HU [auth B4], HV [auth K4], HW [auth A6], HX [auth A6], HY [auth B6], HZ [auth B6], IBA [auth A5], IC [auth A1], ID [auth A1], IDA [auth B5], IE [auth B1], IEA [auth B5], IF [auth B1], IFA [auth L5], IG [auth J1], IH [auth A2], II [auth A2], IJ [auth B2], IK [auth B2], IM [auth A3], IN [auth A3], IO [auth B3], IP [auth B3], IR [auth A4], IS [auth A4], IT [auth B4], IU [auth B4], IV [auth L4], IW [auth A6], IY [auth B6], JAA [auth L6], JBA [auth A5], JC [auth A1], JD [auth A1], JDA [auth B5], JE [auth B1], JF [auth B1], JFA [auth L5], JH [auth A2], JI [auth A2], JJ [auth B2], JK [auth B2], JL [auth K2], JM [auth A3], JN [auth A3], JO [auth B3], JP [auth B3], JQ [auth K3], JR [auth A4], JS [auth A4], JT [auth B4], JU [auth B4], JW [auth A6], JY [auth B6], KAA [auth L6], KBA [auth A5], KC [auth A1], KD [auth A1], KDA [auth B5], KE [auth B1], KF [auth B1], KH [auth A2], KI [auth A2], KJ [auth B2], KK [auth B2], KM [auth A3], KN [auth A3], KO [auth B3], KP [auth B3], KR [auth A4], KT [auth B4], KU [auth B4], KV [auth L4], KW [auth A6], KY [auth B6], LAA [auth L6], LBA [auth A5], LC [auth A1], LD [auth A1], LDA [auth B5], LE [auth B1], LF [auth B1], LG [auth K1], LH [auth A2], LI [auth A2], LJ [auth B2], LK [auth B2], LL [auth L2], LM [auth A3], LN [auth A3], LO [auth B3], LP [auth B3], LQ [auth L3], LR [auth A4], LT [auth B4], LU [auth B4], LV [auth L4], LW [auth A6], LY [auth B6], MBA [auth A5], MC [auth A1], MD [auth A1], MDA [auth B5], ME [auth B1], MF [auth B1], MFA [auth X5], MG [auth L1], MH [auth A2], MI [auth A2], MJ [auth B2], MK [auth B2], MM [auth A3], MN [auth A3], MO [auth B3], MP [auth B3], MQ [auth L3], MR [auth A4], MT [auth B4], MV [auth L4], MW [auth A6], MY [auth B6], NAA [auth M6], NBA [auth A5], NC [auth A1], ND [auth A1], NDA [auth B5], NE [auth B1], NG [auth L1], NH [auth A2], NI [auth A2], NJ [auth B2], NK [auth B2], NM [auth A3], NN [auth A3], NO [auth B3], NP [auth B3], NQ [auth L3], NR [auth A4], NT [auth B4], NW [auth A6], NY [auth B6], OBA [auth A5], OC [auth A1], ODA [auth B5], OE [auth B1], OH [auth A2], OI [auth A2], OJ [auth B2], OK [auth B2], OL [auth L2], OM [auth A3], OO [auth B3], OP [auth B3], OQ [auth L3], OR [auth A4], OT [auth B4], OW [auth A6], OY [auth B6], PAA [auth X6], PBA [auth A5], PC [auth A1], PDA [auth B5], PE [auth B1], PH [auth A2], PI [auth A2], PJ [auth B2], PL [auth L2], PM [auth A3], PO [auth B3], PP [auth B3], PR [auth A4], PT [auth B4], PW [auth A6], PY [auth B6], QAA [auth A5], QBA [auth A5], QC [auth A1], QDA [auth B5], QE [auth B1], QG [auth L1], QH [auth A2], QI [auth A2], QJ [auth B2], QL [auth L2], QM [auth A3], QO [auth B3], QQ [auth M3], QR [auth A4], QT [auth B4], QW [auth A6], QY [auth B6], RAA [auth A5], RBA [auth A5], RC [auth A1], RDA [auth B5], RE [auth B1], RG [auth L1], RH [auth A2], RJ [auth B2], RM [auth A3], RO [auth B3], RR [auth A4], RT [auth B4], RW [auth A6], RX [auth A6], RY [auth B6], SAA [auth A5], SBA [auth A5], SC [auth A1], SCA [auth B5], SDA [auth B5], SE [auth B1], SG [auth L1], SH [auth A2], SJ [auth B2], SL [auth M2], SM [auth A3], SO [auth B3], SR [auth A4], ST [auth B4], SV [auth X4], SW [auth A6], SY [auth B6], TAA [auth A5], TBA [auth A5], TC [auth A1], TCA [auth B5], TDA [auth B5], TE [auth B1], TEA [auth F5], TH [auth A2], TJ [auth B2], TM [auth A3], TO [auth B3], TQ [auth X3], TR [auth A4], TT [auth B4], TV [auth A6], TW [auth A6], TY [auth B6], UAA [auth A5], UBA [auth A5], UC [auth A1], UCA [auth B5], UDA [auth B5], UE [auth B1], UH [auth A2], UJ [auth B2], UL [auth X2], UM [auth A3], UO [auth B3], UQ [auth A4], UR [auth A4], US [auth A4], UT [auth B4], UU [auth B4], UV [auth A6], UW [auth A6], UX [auth B6], UY [auth B6], UZ [auth F6], VAA [auth A5], VBA [auth A5], VC [auth A1], VCA [auth B5], VDA [auth B5], VE [auth B1], VG [auth M1], VH [auth A2], VJ [auth B2], VL [auth A3], VM [auth A3], VO [auth B3], VQ [auth A4], VR [auth A4], VS [auth B4], VT [auth B4], VV [auth A6], VW [auth A6], VX [auth B6], VY [auth B6], WAA [auth A5], WBA [auth A5], WC [auth A1], WCA [auth B5], WDA [auth B5], WE [auth B1], WH [auth A2], WJ [auth B2], WL [auth A3], WM [auth A3], WO [auth B3], WQ [auth A4], WR [auth A4], WS [auth B4], WT [auth B4], WV [auth A6], WW [auth A6], WX [auth B6], WY [auth B6], WZ [auth I6], XAA [auth A5], XBA [auth A5], XC [auth A1], XCA [auth B5], XDA [auth B5], XE [auth B1], XEA [auth J5], XG [auth X1], XH [auth A2], XJ [auth B2], XL [auth A3], XM [auth A3], XO [auth B3], XQ [auth A4], XR [auth A4], XS [auth B4], XT [auth B4], XV [auth A6], XW [auth A6], XX [auth B6], XY [auth B6], YAA [auth A5], YBA [auth A5], YC [auth A1], YCA [auth B5], YD [auth B1], YDA [auth B5], YE [auth B1], YEA [auth J5], YF [auth B1], YG [auth A2], YH [auth A2], YJ [auth B2], YL [auth A3], YM [auth A3], YO [auth B3], YQ [auth A4], YR [auth A4], YS [auth B4], YT [auth B4], YU [auth F4], YV [auth A6], YW [auth A6], YX [auth B6], YY [auth B6], YZ [auth J6], ZAA [auth A5], ZBA [auth A5], ZC [auth A1], ZCA [auth B5], ZD [auth B1], ZDA [auth B5], ZE [auth B1], ZF [auth B1], ZG [auth A2], ZH [auth A2], ZJ [auth B2], ZL [auth A3], ZM [auth A3], ZN [auth B3], ZO [auth B3], ZQ [auth A4], ZR [auth A4], ZS [auth B4], ZT [auth B4], ZV [auth A6], ZW [auth A6], ZX [auth B6], ZY [auth B6], ZZ [auth J6]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG	OZ [auth B6], QEA [auth B5], TU [auth B4], VF [auth B1], WK [auth B2], WP [auth B3]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG	NFA [auth X5], OCA [auth A5], PCA [auth A5], PX [auth A6], PZ [auth B6], QX [auth A6], RS [auth A4], RV [auth X4], SQ [auth X3], SS [auth A4], VD [auth A1], VN [auth A3], WD [auth A1], WF [auth B1], WN [auth A3], XK [auth B2], YI [auth A2], ZI [auth A2]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR	AFA [auth J5], AQ [auth F3], AV [auth F4], BAA [auth J6], BFA [auth J5], BL [auth F2], BV [auth I4], CAA [auth J6], CQ [auth F3], CV [auth I4], DG [auth F1], DL [auth F2], DQ [auth I3], EAA [auth L6], EFA [auth L5], EQ [auth I3], FG [auth I1], FL [auth I2], FV [auth J4], GG [auth I1], GV [auth J4], HAA [auth L6], HL [auth J2], HQ [auth J3], ICA [auth A5], IL [auth J2], IQ [auth J3], JCA [auth A5], JG [auth J1], JX [auth A6], JZ [auth B6], KCA [auth A5], KEA [auth B5], KFA [auth L5], KG [auth J1], KL [auth L2], KQ [auth L3], KX [auth A6], KZ [auth B6], LCA [auth A5], LEA [auth B5], LFA [auth M5], LS [auth A4], LX [auth A6], LZ [auth B6], MAA [auth L6], MCA [auth A5], MEA [auth B5], ML [auth L2], MS [auth A4], MX [auth A6], MZ [auth B6], NCA [auth A5], NEA [auth B5], NS [auth A4], NU [auth B4], NV [auth L4], NX [auth A6], NZ [auth B6], OAA [auth M6], OEA [auth B5], OF [auth B1], OG [auth L1], OS [auth A4], OU [auth B4], OX [auth A6], PD [auth A1], PEA [auth B5], PF [auth B1], PN [auth A3], PQ [auth L3], PS [auth A4], PU [auth B4], PV [auth L4], QCA [auth A5], QD [auth A1], QF [auth B1], QK [auth B2], QN [auth A3], QS [auth A4], QU [auth B4], QV [auth M4], QZ [auth B6], RD [auth A1], RF [auth B1], RK [auth B2], RL [auth L2], RN [auth A3], RP [auth B3], RQ [auth M3], RU [auth B4], SD [auth A1], SF [auth B1], SI [auth A2], SK [auth B2], SN [auth A3], SP [auth B3], SU [auth B4], SX [auth A6], TD [auth A1], TF [auth B1], TI [auth A2], TK [auth B2], TL [auth M2], TN [auth A3], TP [auth B3], TZ [auth F6], UD [auth A1], UEA [auth F5], UF [auth B1], UG [auth L1], UI [auth A2], UK [auth B2], UN [auth A3], UP [auth B3], VEA [auth I5], VI [auth A2], VK [auth B2], VP [auth B3], VZ [auth F6], WEA [auth I5], WG [auth M1], WI [auth A2], XF [auth B1], XI [auth A2], XP [auth B3], XU [auth F4], XZ [auth I6], YK [auth B2], YN [auth A3], ZEA [auth J5], ZU [auth F4]	BETA-CAROTENE C40 H56 OENHQHLEOONYIE-JLTXGRSLSA-N
PQN	HCA [auth A5], IX [auth A6], IZ [auth B6], JEA [auth B5], KS [auth A4], MU [auth B4], NF [auth B1], OD [auth A1], ON [auth A3], PK [auth B2], QP [auth B3], RI [auth A2]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4	AG [auth C1], AJ [auth A2], AL [auth C2], BG [auth C1], RCA [auth A5], REA [auth C5], RZ [auth C6], SEA [auth C5], SZ [auth C6], TS [auth A4], TX [auth B6], VU [auth C4], WU [auth C4], XD [auth A1], XN [auth A3], YP [auth C3], ZK [auth C2], ZP [auth C3]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
FES	OFA [auth P1], PFA [auth P2], QFA [auth P3], RFA [auth P4], SFA [auth P6], TFA [auth P5]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
CA	IAA [auth L6], JV [auth L4], NL [auth L2], OV [auth L4], PG [auth L1], TG [auth L1]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.20 Å
• R-Value Free:  0.377 (Depositor), 0.380 (DCC) 
• R-Value Work:  0.353 (Depositor), 0.360 (DCC) 
• R-Value Observed: 0.354 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 214.101	α = 90
b = 239.668	β = 101.08
c = 265.605	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Kubota-Kawai, H., Mutoh, R., Shinmura, K., Setif, P., Nowaczyk, M., Roegner, M., Ikegami, T., Tanaka, T., Kurisu, G.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	GS016
Japan science and technology agency	Japan	--
Japan Society for the Promotion of Science	Japan	13J03550

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-04-25
  Changes: Data collection, Database references
• Version 2.0: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
• Version 2.1: 2024-10-23
  Changes: Structure summary