4G8S | pdb_00004g8s

Crystal Structure Of a Putative Nitroreductase from Geobacter sulfurreducens PCA (Target PSI-013445)

• PDB DOI: https://doi.org/10.2210/pdb4G8S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacter sulfurreducens PCA
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-23 Released: 2012-08-08 
• Deposition Author(s): Kumar, P.R., Bhosle, R., Hillerich, B., Seidel, R., Toro, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Literature

Crystal structure of a nitroreductase from Geobacter sulfurreducens PCA

Kumar, P.R., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Gizzi, A., Glen, S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Washington, E., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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)

Macromolecule Content 

• Total Structure Weight: 47.86 kDa 
• Atom Count: 2,985 
• Modeled Residue Count: 363 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitroreductase family protein	A, B	210	Geobacter sulfurreducens PCA	Mutation(s): 0  Gene Names: GSU0217
UniProt
Find proteins for Q74GM9 (Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA)) Explore Q74GM9  Go to UniProtKB:  Q74GM9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	C [auth A], D [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.759	α = 90
b = 73.759	β = 90
c = 169.472	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-08 
Deposition Author(s): Kumar, P.R., Bhosle, R., Hillerich, B., Seidel, R., Toro, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary