3GM6

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate

PDB DOI: https://doi.org/10.2210/pdb3GM6/pdb

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

Deposited: 2009-03-13 Released: 2009-08-04
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Filimonenkov, A.A., Dorovatovsky, P.V., Tikhonova, T.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.172
R-Value Work: 0.159
R-Value Observed: 0.159

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate

Trofimov, A.A., Polyakov, K.M., Boiko, K.M., Filimonenkov, A.A., Dorovatovskii, P.V., Tikhonova, T.V., Popov, V.O., Koval'chuk, M.V.

(2010) Crystallogr Rep 55: 58-64

DOI: https://doi.org/10.1134/S1063774510010104

Macromolecule Content

Total Structure Weight: 129.62 kDa
Atom Count: 10,071
Modelled Residue Count: 1,042
Deposited Residue Count: 1,050
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	525	Thioalkalivibrio nitratireducens	Mutation(s): 0 EC: 1.7.2.2
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 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 O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] 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 V [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 O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] 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 V [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [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 O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [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], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [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 O [auth B] Focus chain P [auth B] Focus chain Q [auth B] 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] 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 O [auth B] Focus chain P [auth B] Focus chain Q [auth B] 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]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain Z [auth B]	Z [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Y [auth B]	M [auth A], N [auth A], Y [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain W [auth B]	K [auth A], W [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain W [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B]	L [auth A], X [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain X [auth B] Interactions & Density Focus chain L [auth A] Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.172
R-Value Work: 0.159
R-Value Observed: 0.159
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.56	α = 90
b = 196.56	β = 90
c = 196.56	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	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: 2009-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary