5B1K | pdb_00005b1k

Crystal structure of the chloride-bound form of blue copper nitrite reductase

PDB DOI: https://doi.org/10.2210/pdb5B1K/pdb

Classification: OXIDOREDUCTASE
Organism(s): Achromobacter xylosoxidans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-12-04 Released: 2016-11-23
Deposition Author(s): Nojiri, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.173 (Depositor), 0.182 (DCC)
R-Value Work:
0.149 (Depositor), 0.159 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 37.22 kDa
Atom Count: 2,899
Modeled Residue Count: 334
Deposited Residue Count: 337
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	337	Achromobacter xylosoxidans	Mutation(s): 0 Gene Names: nir, nirK, ERS451415_02178 EC: 1.7.2.1
UniProt
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Explore O68601 Go to UniProtKB: O68601
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O68601
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.173 (Depositor), 0.182 (DCC)
R-Value Work: 0.149 (Depositor), 0.159 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.703	α = 90
b = 104.703	β = 90
c = 63.073	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-11-23

Deposition Author(s):

Nojiri, M.

Revision History (Full details and data files)

Version 1.0: 2016-11-23
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

5B1K | pdb_00005b1k

Crystal structure of the chloride-bound form of blue copper nitrite reductase

Literature

Structure and function of copper nitrite reductase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand