4L38

Nitrite complex of TvNiR, low dose data set

PDB DOI: https://doi.org/10.2210/pdb4L38/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thioalkalivibrio nitratireducens DSM 14787
Mutation(s): No

Deposited: 2013-06-05 Released: 2014-07-16
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Lazarenko, V.A., Popov, A.N., Tikhonova, T.V., Tikhonov, A.V., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.170
R-Value Work: 0.153
R-Value Observed: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Investigation of the X-ray-induced nitrite reduction catalysed by cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens

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

To be published.

Macromolecule Content

Total Structure Weight: 129.09 kDa
Atom Count: 10,419
Modelled Residue Count: 1,040
Deposited Residue Count: 1,040
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	520	Thioalkalivibrio nitratireducens DSM 14787	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [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 U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [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 U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [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 U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] C [auth A] D [auth A] E [auth A] AA [auth B], BA [auth B], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] 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 U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] 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 U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain N [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain N [auth A]	FA [auth B], N [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain FA [auth B] Focus chain N [auth A] Interactions & Density Focus chain FA [auth B] Focus chain N [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain R [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain R [auth A]	IA [auth B], R [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain IA [auth B] Focus chain R [auth A] Interactions & Density Focus chain IA [auth B] Focus chain R [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	GA [auth B], HA [auth B], O [auth A], P [auth A], Q [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
NO2 Query on NO2 Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	CA [auth B] JA [auth B] K [auth A] KA [auth B] S [auth A] CA [auth B], JA [auth B], K [auth A], KA [auth B], S [auth A], T [auth A]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain CA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain CA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain S [auth A] Focus chain T [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	DA [auth B], EA [auth B], L [auth A], M [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain L [auth A] Focus chain M [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.170
R-Value Work: 0.153
R-Value Observed: 0.154
Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.97	α = 90
b = 193.97	β = 90
c = 193.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary