1FGJ

X-RAY STRUCTURE OF HYDROXYLAMINE OXIDOREDUCTASE

PDB DOI: https://doi.org/10.2210/pdb1FGJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Nitrosomonas europaea
Mutation(s): No

Deposited: 1997-03-03 Released: 1998-03-04
Deposition Author(s): Tanaka, N., Igarashi, N., Moriyama, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.309
R-Value Work: 0.230
R-Value Observed: 0.230

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea.

Igarashi, N., Moriyama, H., Fujiwara, T., Fukumori, Y., Tanaka, N.

(1997) Nat Struct Biol 4: 276-284

PubMed: 9095195 Search on PubMed
DOI: https://doi.org/10.1038/nsb0497-276
Primary Citation of Related Structures:
1FGJ

PubMed Abstract:
The 2.8 A crystal structure of hydroxylamine oxidoreductase of a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea, is described. Twenty-four haems lie in the centre bottom of the trimeric molecule, localized in four clusters within each monomer. The haem clusters within the trimer are aligned to form a ring that has inlet and outlet sites. The inlet is occupied by a novel haem, P460, and there are two possible outlet sites per monomer formed by paired haems lying within a cavity or cleft on the protein surface. The structure suggests pathways by which electron transfer may occur through the precisely arranged haems and provides a framework for the interpretation of previous and future biochemical and genetic observations.

Organizational Affiliation

Department of Life Science, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.

Macromolecule Content

Total Structure Weight: 133.34 kDa
Atom Count: 8,648
Modelled Residue Count: 998
Deposited Residue Count: 1,092
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROXYLAMINE OXIDOREDUCTASE	A, B	546	Nitrosomonas europaea	Mutation(s): 0 EC: 1.7.3.4 (PDB Primary Data), 1.7.2.6 (UniProt), 1.7.2.9 (UniProt)
UniProt
Find proteins for Q50925 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q50925 Go to UniProtKB: Q50925
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q50925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	F [auth A], N [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B]
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B]	C [auth A] D [auth A] E [auth A] G [auth A] H [auth A] C [auth A], D [auth A], E [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.309
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.2	α = 90
b = 96.2	β = 90
c = 265.7	γ = 120

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 1998-03-04

Deposition Author(s):

Tanaka, N.

Igarashi, N.

Moriyama, H.

Revision History (Full details and data files)

Version 1.0: 1998-03-04
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary