3G14 | pdb_00003g14

Crystal structure of nitroreductase family protein (YP_877874.1) from Clostridium novyi NT at 1.75 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3G14/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium novyi NT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-29 Released: 2009-02-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of nitroreductase family protein (YP_877874.1) from Clostridium novyi NT at 1.75 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)

Macromolecule Content 

• Total Structure Weight: 44.59 kDa 
• Atom Count: 3,142 
• Modeled Residue Count: 355 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitroreductase family protein	A, B	193	Clostridium novyi NT	Mutation(s): 0  Gene Names: noxC, NT01CX_1801, YP_877874.1 EC: 1
UniProt
Find proteins for A0PZS2 (Clostridium novyi (strain NT)) Explore A0PZS2  Go to UniProtKB:  A0PZS2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	D [auth A], F [auth B], G [auth B], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.75 Å
• R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33G14

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.35	α = 90
b = 44.95	β = 93.72
c = 66.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: 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
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary