3X1F

H294M mutant of copper-containing nitrite reductase from Geobacillus thermodenitrificans

• PDB DOI: https://doi.org/10.2210/pdb3X1F/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Geobacillus thermodenitrificans NG80-2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-11-16 Released: 2015-11-18 
• Deposition Author(s): Fukuda, Y., Inoue, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.115 
• R-Value Work: 0.092 
• R-Value Observed: 0.093 

Starting Model: experimental

Literature

Structural evidence of the flexibility of the CuM site

Fukuda, Y., Inoue, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.34 kDa 
• Atom Count: 2,932 
• Modelled Residue Count: 296 
• Deposited Residue Count: 352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite reductase	A	352	Geobacillus thermodenitrificans NG80-2	Mutation(s): 1  Gene Names: nirK EC: 1.7.2.1
UniProt
Find proteins for A4IL26 (Geobacillus thermodenitrificans (strain NG80-2)) Explore A4IL26  Go to UniProtKB:  A4IL26

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	K [auth A], L [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
CU	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACY	I [auth A], J [auth A], M [auth A], N [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.115 
• R-Value Work: 0.092 
• R-Value Observed: 0.093 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.977	α = 90
b = 114.977	β = 90
c = 84.138	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Fukuda, Y., Inoue, T.

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description