3E9M | pdb_00003e9m

Crystal Structure of an oxidoreductase from Enterococcus faecalis

• PDB DOI: https://doi.org/10.2210/pdb3E9M/pdb

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


• Deposited: 2008-08-22 Released: 2008-10-14 
• Deposition Author(s): Damodharan, L., 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: 2.70 Å
• R-Value Free: 
  0.294 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Crystal Structure of an oxidoreductase from Enterococcus faecalis

Damodharan, L., 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 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 148.59 kDa 
• Atom Count: 9,967 
• Modeled Residue Count: 1,276 
• Deposited Residue Count: 1,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B, C, D	330	Enterococcus faecalis	Mutation(s): 0  Gene Names: EF_0827
UniProt
Find proteins for Q837L0 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q837L0  Go to UniProtKB:  Q837L0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.294 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.918	α = 90
b = 146.925	β = 100.84
c = 80.531	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary