7R2U

CRYSTAL STRUCTURE OF AS-ISOLATED Q262N MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

PDB DOI: https://doi.org/10.2210/pdb7R2U/pdb

Classification: OXIDOREDUCTASE
Organism(s): Ralstonia pickettii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-02-05 Released: 2023-02-15
Deposition Author(s): Petchyam, N., Antonyuk, S., Hasnain, S.S.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.153
R-Value Work: 0.105
R-Value Observed: 0.108

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and biochemical studies of three-domain haem CuNiR from Ralstonia pickettii mutants

Petchyam, N., Antonyuk, S., Hasnain, S.S.

To be published.

Macromolecule Content

Total Structure Weight: 50.68 kDa
Atom Count: 4,566
Modelled Residue Count: 457
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	468	Ralstonia pickettii	Mutation(s): 1 Gene Names: RP6297_03937 EC: 1.7.2.1
UniProt
Find proteins for I6NAW4 (Ralstonia pickettii) Explore I6NAW4 Go to UniProtKB: I6NAW4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I6NAW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC (Subject of Investigation/LOI) Query on HEC Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CU Query on CU Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.153
R-Value Work: 0.105
R-Value Observed: 0.108
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.65	α = 90
b = 127.65	β = 90
c = 86.29	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
AutoProcess	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-02-15

Deposition Author(s):

Funding Organization	Location	Grant Number
UK Research and Innovation (UKRI)	United Kingdom	BB/N013972/1
UK Research and Innovation (UKRI)	United Kingdom	BB/L006960/1

Revision History (Full details and data files)

Version 1.0: 2023-02-15
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.