3FHL | pdb_00003fhl

Crystal structure of a putative oxidoreductase from bacteroides fragilis nctc 9343

• PDB DOI: https://doi.org/10.2210/pdb3FHL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacteroides fragilis NCTC 9343
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-09 Released: 2008-12-23 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Crystal Structure of a Putative Oxidoreductase from Bacteroides Fragilis Nctc 9343

Patskovsky, Y., Ramagopal, U., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 164.3 kDa 
• Atom Count: 11,782 
• Modeled Residue Count: 1,319 
• Deposited Residue Count: 1,448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B, C, D	362	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF2340
UniProt
Find proteins for Q5LCX7 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LCX7  Go to UniProtKB:  Q5LCX7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	F [auth A], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.215 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.258	α = 90
b = 127.367	β = 112.01
c = 79.889	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-12-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references, Refinement description