Macromolecule Content

Total Structure Weight: 87.05 kDa
Atom Count: 6055
Residue Count: 792
Unique protein chains: 2

5B1J

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

DOI: 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.233
R-Value Work: 0.171
R-Value Observed: 0.175

wwPDB Validation3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure and Function of Copper Nitrite Reductase

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

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Copper-containing nitrite reductase	A, B	336	Achromobacter xylosoxidans	Mutation(s): 0 Gene Names: nir, nirK, ERS451415_02178 EC: 1.7.2.1
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Go to UniProtKB: O68601
Protein Feature View Full Protein Feature View for O68601

Find similar proteins by: Sequence | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Blue copper protein	C	124	Hyphomicrobium denitrificans	Mutation(s): 0 Gene Names: paz
Find proteins for A7VL37 (Hyphomicrobium denitrificans) Go to UniProtKB: A7VL37
Protein Feature View Full Protein Feature View for A7VL37

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download CCD File	A, B, C	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.233
R-Value Work: 0.171
R-Value Observed: 0.175
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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2015-12-04
Released Date: 2016-11-23

Deposition Author(s):

Revision History

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.