3OC4 | pdb_00003oc4

Crystal Structure of a pyridine nucleotide-disulfide family oxidoreductase from the Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb3OC4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-09 Released: 2010-10-06 
• Deposition Author(s): Kumaran, D., Baumann, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Crystal Structure of a pyridine nucleotide-disulfide family oxidoreductase from the Enterococcus faecalis V583

Kumaran, D., Baumann, K., Burley, S.K., Swaminathan, S.

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: 103.36 kDa 
• Atom Count: 6,914 
• Modeled Residue Count: 843 
• Deposited Residue Count: 904 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, pyridine nucleotide-disulfide family	A, B	452	Enterococcus faecalis	Mutation(s): 0  Gene Names: EF1932, EF_1932
UniProt
Find proteins for Q833L5 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q833L5  Go to UniProtKB:  Q833L5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], E [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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: 2.60 Å
• R-Value Free:  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.693	α = 90
b = 213.693	β = 90
c = 149.259	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Kumaran, D., Baumann, K., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary