2FG9 | pdb_00002fg9

CRYSTAL STRUCTURE OF A PUTATIVE 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE PROTEIN (BT_3078) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.20 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2FG9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-12-21 Released: 2006-01-10 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of (np_811990.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

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,PQS (software)

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content 

• Total Structure Weight: 21.92 kDa 
• Atom Count: 1,438 
• Modeled Residue Count: 166 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-nitroimidazole antibiotic resistance protein	A	178	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 8  Gene Names: np_811990.1
UniProt
Find proteins for Q8A377 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A377  Go to UniProtKB:  Q8A377

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

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: 2.20 Å
• R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32FG9

Space Group: I 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134	α = 90
b = 134	β = 90
c = 134	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-10 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2006-01-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-25
  Changes: Author supporting evidence
• Version 1.4: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary