9FOM | pdb_00009fom

CRYSTAL STRUCTURE OF AS-ISOLATED F295L MUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

PDB DOI: https://doi.org/10.2210/pdb9FOM/pdb

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

Deposited: 2024-06-12 Released: 2025-06-25
Deposition Author(s): Petchyam, N., Antonyuk, S.V., Hasnain, S.S.
Funding Organization(s): UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free:
0.139 (Depositor), 0.140 (DCC)
R-Value Work:
0.114 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

CRYSTAL STRUCTURE OF AS-ISOLATED F295LMUTANT OF THREE-DOMAIN HEME-CU NITRITE REDUCTASE FROM RALSTONIA PICKETTII

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

To be published.

Macromolecule Content

Total Structure Weight: 50.66 kDa
Atom Count: 4,656
Modeled Residue Count: 456
Deposited Residue Count: 468
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A	468	Ralstonia pickettii	Mutation(s): 1 Gene Names: nirK, D7S62_04310 EC: 1.7.2.1
UniProt
Find proteins for B2UHR8 (Ralstonia pickettii (strain 12J)) Explore B2UHR8 Go to UniProtKB: B2UHR8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2UHR8
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] mmCIF 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 (Subject of Investigation/LOI) 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] mmCIF format, chain B [auth A] mmCIF 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: 1.16 Å
R-Value Free: 0.139 (Depositor), 0.140 (DCC)
R-Value Work: 0.114 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.257	α = 90
b = 128.257	β = 90
c = 86.194	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
Coot	model building
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

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: 2025-06-25
Type: Initial release

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