3S7W

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine

PDB DOI: https://doi.org/10.2210/pdb3S7W/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thioalkalivibrio nitratireducens
Mutation(s): No

Deposited: 2011-05-27 Released: 2011-07-27
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Tikhonova, T.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.172
R-Value Work: 0.153
R-Value Observed: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 in a complex with hydroxylamine

Trofimov, A.A., Polyakov, K.M., Tikhonova, T.V., Popov, V.O.

To be published.

Macromolecule Content

Total Structure Weight: 128.55 kDa
Atom Count: 10,174
Modelled Residue Count: 1,038
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eight-heme nitrite reductase	A, B	519	Thioalkalivibrio nitratireducens	Mutation(s): 0
UniProt
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2)) Explore L0DSL2 Go to UniProtKB: L0DSL2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	L0DSL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [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 R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [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 R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain N [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain N [auth A]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] M [auth A] BA [auth B], CA [auth B], DA [auth B], EA [auth B], M [auth A], N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
NO2 Query on NO2 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Z [auth B]	K [auth A], Z [auth B]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain Z [auth B]
AZI Query on AZI Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain GA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain GA [auth B]	GA [auth B], Q [auth A]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth B] Focus chain Q [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain P [auth A] SDF format, chain AA [auth B] SDF format, chain L [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain L [auth A]	AA [auth B], FA [auth B], L [auth A], P [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain FA [auth B] Focus chain L [auth A] Focus chain P [auth A] Interactions & Density Focus chain AA [auth B] Focus chain FA [auth B] Focus chain L [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.172
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 194.89	α = 90
b = 194.89	β = 90
c = 194.89	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description