3HA2 | pdb_00003ha2

Crystal Structure of Protein (NADPH-quinone reductase) from P.pentosaceus, Northeast Structural Genomics Consortium Target PtR24A

• PDB DOI: https://doi.org/10.2210/pdb3HA2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pediococcus pentosaceus ATCC 25745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-04-30 Released: 2009-05-26 
• Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Northeast Structural Genomics Consortium Target PtR24A

Kuzin, A., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.46 kDa 
• Atom Count: 2,877 
• Modelled Residue Count: 336 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-quinone reductase	A, B	177	Pediococcus pentosaceus ATCC 25745	Mutation(s): 0  Gene Names: PEPE_1665
UniProt
Find proteins for Q03DN6 (Pediococcus pentosaceus (strain ATCC 25745 / CCUG 21536 / LMG 10740 / 183-1w)) Explore Q03DN6  Go to UniProtKB:  Q03DN6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	C [auth A], D [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.228 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.74	α = 90
b = 65.74	β = 90
c = 183.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Kuzin, A., Su, M., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary