1VQ9

The structure of CCA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history. 


Literature

Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.

Schmeing, T.M., Huang, K.S., Kitchen, D.E., Strobel, S.A., Steitz, T.A.

(2005) Mol Cell 20: 437-448

  • DOI: https://doi.org/10.1016/j.molcel.2005.09.006
  • Primary Citation of Related Structures:  
    1VQ4, 1VQ5, 1VQ8, 1VQ9, 1VQK, 1VQL, 1VQM, 1VQO, 1VQP

  • PubMed Abstract: 

    Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

    • Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2PD [auth A]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3PE [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4EF [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PG [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PH [auth E]178Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AEI [auth F]120Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOGJ [auth G]348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EK [auth H]171Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PL [auth J]145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PM [auth K]132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PN [auth L]165Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S Ribosomal Protein L15EO [auth M]195Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PP [auth N]187Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eQ [auth O]116Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19ER [auth P]149Haloarcula marismortuiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eS [auth Q]96Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PT [auth R]155Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PU [auth S]85Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PV [auth T]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24EW [auth U]66Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PX [auth V]71Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PY [auth W]154Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eZ [auth X]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32EAA [auth Y]241Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37AeBA [auth Z]83Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eCA [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eDA [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44EEA [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11PFA [auth I]162Haloarcula marismortuiMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S ribosomal rnaA [auth 0]2,922Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S ribosomal RNAB [auth 9]122Haloarcula marismortui
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-R(*CP*CP*AP*(PHE)*(ACA))-3'C [auth 4]5N/A
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPS
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IK [auth 4]SPARSOMYCIN
C13 H19 N3 O5 S2
XKLZIVIOZDNKEQ-CLQLPEFOSA-N
CD
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AM [auth 1],
EM [auth 3],
LL [auth O],
WL [auth U],
ZL [auth Z]		CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SR
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AH [auth 0]
AI [auth 0]
AJ [auth 0]
AK [auth 0]
BH [auth 0]
AH [auth 0],
AI [auth 0],
AJ [auth 0],
AK [auth 0],
BH [auth 0],
BI [auth 0],
BJ [auth 0],
BK [auth 0],
BM [auth 1],
CH [auth 0],
CI [auth 0],
CJ [auth 0],
CM [auth 1],
DH [auth 0],
DI [auth 0],
DJ [auth 0],
EH [auth 0],
EI [auth 0],
EJ [auth 0],
FH [auth 0],
FI [auth 0],
FJ [auth 0],
FK [auth 9],
GH [auth 0],
GI [auth 0],
GJ [auth 0],
GK [auth 9],
GM [auth 3],
HH [auth 0],
HI [auth 0],
HJ [auth 0],
HK [auth 9],
HL [auth L],
IH [auth 0],
II [auth 0],
IJ [auth 0],
JG [auth 0],
JH [auth 0],
JI [auth 0],
JJ [auth 0],
KG [auth 0],
KH [auth 0],
KI [auth 0],
KJ [auth 0],
LG [auth 0],
LH [auth 0],
LI [auth 0],
LJ [auth 0],
MG [auth 0],
MH [auth 0],
MI [auth 0],
MJ [auth 0],
MK [auth A],
NG [auth 0],
NH [auth 0],
NI [auth 0],
NJ [auth 0],
NK [auth A],
OG [auth 0],
OH [auth 0],
OI [auth 0],
OJ [auth 0],
OK [auth A],
PG [auth 0],
PH [auth 0],
PI [auth 0],
PJ [auth 0],
PK [auth A],
QG [auth 0],
QH [auth 0],
QI [auth 0],
QJ [auth 0],
RG [auth 0],
RH [auth 0],
RI [auth 0],
RJ [auth 0],
RL [auth R],
SG [auth 0],
SH [auth 0],
SI [auth 0],
SJ [auth 0],
TG [auth 0],
TH [auth 0],
TI [auth 0],
TJ [auth 0],
TL [auth S],
UG [auth 0],
UH [auth 0],
UI [auth 0],
UJ [auth 0],
UK [auth B],
VG [auth 0],
VH [auth 0],
VI [auth 0],
VJ [auth 0],
VK [auth B],
WG [auth 0],
WH [auth 0],
WI [auth 0],
WJ [auth 0],
XG [auth 0],
XH [auth 0],
XI [auth 0],
XJ [auth 0],
YG [auth 0],
YH [auth 0],
YI [auth 0],
YJ [auth 0],
YK [auth F],
ZG [auth 0],
ZH [auth 0],
ZI [auth 0],
ZJ [auth 0],
ZK [auth H]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
K
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OD [auth 0],
PD [auth 0]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
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AG [auth 0]
BG [auth 0]
BL [auth J]
CG [auth 0]
CL [auth J]
AG [auth 0],
BG [auth 0],
BL [auth J],
CG [auth 0],
CL [auth J],
DG [auth 0],
DL [auth J],
EG [auth 0],
FG [auth 0],
FL [auth K],
FM [auth 3],
GG [auth 0],
GL [auth L],
HG [auth 0],
IG [auth 0],
JL [auth M],
KL [auth N],
LK [auth A],
ML [auth O],
QL [auth R],
TK [auth B],
YL [auth Y]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
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AB [auth 0]
AC [auth 0]
AD [auth 0]
BB [auth 0]
BC [auth 0]
AB [auth 0],
AC [auth 0],
AD [auth 0],
BB [auth 0],
BC [auth 0],
BD [auth 0],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CK [auth 9],
DB [auth 0],
DC [auth 0],
DD [auth 0],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EL [auth K],
FB [auth 0],
FC [auth 0],
FD [auth 0],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HD [auth 0],
IA [auth 0],
IB [auth 0],
IC [auth 0],
ID [auth 0],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JD [auth 0],
JK [auth 4],
KA [auth 0],
KB [auth 0],
KC [auth 0],
KD [auth 0],
KK [auth A],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LD [auth 0],
MA [auth 0],
MB [auth 0],
MC [auth 0],
MD [auth 0],
NA [auth 0],
NB [auth 0],
NC [auth 0],
ND [auth 0],
OA [auth 0],
OB [auth 0],
OC [auth 0],
PA [auth 0],
PB [auth 0],
PC [auth 0],
QA [auth 0],
QB [auth 0],
QC [auth 0],
QK [auth B],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RK [auth B],
SA [auth 0],
SB [auth 0],
SC [auth 0],
TA [auth 0],
TB [auth 0],
TC [auth 0],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UL [auth T],
VA [auth 0],
VB [auth 0],
VC [auth 0],
WA [auth 0],
WB [auth 0],
WC [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XL [auth Y],
YA [auth 0],
YB [auth 0],
YC [auth 0],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
AE [auth 0]
AF [auth 0]
AL [auth J]
BE [auth 0]
BF [auth 0]
AE [auth 0],
AF [auth 0],
AL [auth J],
BE [auth 0],
BF [auth 0],
CE [auth 0],
CF [auth 0],
DE [auth 0],
DF [auth 0],
DK [auth 9],
DM [auth 3],
EE [auth 0],
EF [auth 0],
EK [auth 9],
FE [auth 0],
FF [auth 0],
GE [auth 0],
GF [auth 0],
HE [auth 0],
HF [auth 0],
IE [auth 0],
IF [auth 0],
IL [auth M],
JE [auth 0],
JF [auth 0],
KE [auth 0],
KF [auth 0],
LE [auth 0],
LF [auth 0],
ME [auth 0],
MF [auth 0],
NE [auth 0],
NF [auth 0],
NL [auth Q],
OE [auth 0],
OF [auth 0],
OL [auth R],
PE [auth 0],
PF [auth 0],
PL [auth R],
QD [auth 0],
QE [auth 0],
QF [auth 0],
RD [auth 0],
RE [auth 0],
RF [auth 0],
SD [auth 0],
SE [auth 0],
SF [auth 0],
SK [auth B],
SL [auth S],
TD [auth 0],
TE [auth 0],
TF [auth 0],
UD [auth 0],
UE [auth 0],
UF [auth 0],
VD [auth 0],
VE [auth 0],
VF [auth 0],
VL [auth T],
WD [auth 0],
WE [auth 0],
WF [auth 0],
WK [auth C],
XD [auth 0],
XE [auth 0],
XF [auth 0],
XK [auth D],
YD [auth 0],
YE [auth 0],
YF [auth 0],
ZD [auth 0],
ZE [auth 0],
ZF [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.821α = 90
b = 298.596β = 90
c = 574.06γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations