3FD8 | pdb_00003fd8

Crystal Structure of an oxidoreductase from Enterococcus faecalis

• PDB DOI: https://doi.org/10.2210/pdb3FD8/pdb

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


• Deposited: 2008-11-25 Released: 2009-02-03 
• 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: 2.45 Å
• R-Value Free: 
  0.240 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal Structure of an oxidoreductase from Enterococcus faecalis

Damodhran, L., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 246.6 kDa 
• Atom Count: 17,472 
• Modeled Residue Count: 2,090 
• Deposited Residue Count: 2,154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase, Gfo/Idh/MocA family	A, B, C, D, E, F	359	Enterococcus faecalis	Mutation(s): 0  Gene Names: EF_1244
UniProt
Find proteins for Q835X4 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q835X4  Go to UniProtKB:  Q835X4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G [auth B], H [auth C], I [auth F]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.240 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.573	α = 90
b = 151.321	β = 90
c = 161.317	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-03
  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: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-11-20
  Changes: Structure summary