5B1J | pdb_00005b1j

Crystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin

• PDB DOI: https://doi.org/10.2210/pdb5B1J/pdb

• Classification: OXIDOREDUCTASE/ELECTRON TRANSPORT
• Organism(s): Achromobacter xylosoxidans, Hyphomicrobium denitrificans
• Mutation(s): No 


• Deposited: 2015-12-04 Released: 2016-11-23 
• Deposition Author(s): Nojiri, M., Koteishi, H., Yoneda, R., Hira, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structure and Function of Copper Nitrite Reductase

Nojiri, M.

(2016) Metalloenzymes In Denitrification: Applications And Environmental Impacts : 91-113

• DOI: https://doi.org/10.1039/9781782623762-00091

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 87.05 kDa 
• Atom Count: 6,055 
• Modeled Residue Count: 792 
• Deposited Residue Count: 796 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B	336	Achromobacter xylosoxidans	Mutation(s): 0  EC: 1.7.2.1
UniProt
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Explore O68601  Go to UniProtKB:  O68601

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Blue copper protein	C	124	Hyphomicrobium denitrificans	Mutation(s): 0
UniProt
Find proteins for A7VL37 (Hyphomicrobium denitrificans) Explore A7VL37  Go to UniProtKB:  A7VL37

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.233 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.226	α = 90
b = 153.226	β = 90
c = 153.226	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Nojiri, M., Koteishi, H., Yoneda, R., Hira, D.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description