3HOI

Crystal structure of FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 (YP_212631.1) from Bacteroides fragilis NCTC 9343 at 1.55 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3HOI/pdb

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


• Deposited: 2009-06-02 Released: 2009-06-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.187 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Literature

Crystal structure of FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 (YP_212631.1) from Bacteroides fragilis NCTC 9343 at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

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 Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 22.27 kDa 
• Atom Count: 1,891 
• Modelled Residue Count: 193 
• Deposited Residue Count: 193 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent nitroreductase BF3017	A	193	Bacteroides fragilis NCTC 9343	Mutation(s): 0  Gene Names: BF3017, YP_212631.1
UniProt
Find proteins for Q5LB10 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow)) Explore Q5LB10  Go to UniProtKB:  Q5LB10

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FLC	F [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNL	C [auth A]	Unknown ligand QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.187 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.18430/M33HOI

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.873	α = 90
b = 48.873	β = 90
c = 295.194	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations