4DN2 | pdb_00004dn2

CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15

• PDB DOI: https://doi.org/10.2210/pdb4DN2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacter metallireducens GS-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-08 Released: 2012-02-22 
• Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.194 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

CRYSTAL STRUCTURE OF putative Nitroreductase from Geobacter metallireducens GS-15

Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., 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)

Macromolecule Content 

• Total Structure Weight: 47.36 kDa 
• Atom Count: 3,233 
• Modeled Residue Count: 381 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitroreductase	A, B	208	Geobacter metallireducens GS-15	Mutation(s): 0  Gene Names: ABB33053.1, Gmet_2835
UniProt
Find proteins for Q39RS1 (Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15)) Explore Q39RS1  Go to UniProtKB:  Q39RS1

Small Molecules

Ligands 1 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

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: 1.50 Å
• R-Value Free:  0.194 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.884	α = 90
b = 64.161	β = 98.14
c = 61.384	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary