3OWM | pdb_00003owm

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

PDB DOI: https://doi.org/10.2210/pdb3OWM/pdb

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

Deposited: 2010-09-20 Released: 2011-10-26
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Tikhonova, T.V., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.154 (Depositor), 0.164 (DCC)
R-Value Work:
0.139 (Depositor), 0.151 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase

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

To be published.

Macromolecule Content

Total Structure Weight: 132.36 kDa
Atom Count: 10,414
Modeled Residue Count: 1,038
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eight-heme nitrite reductase	A, B	519	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	L0DSL2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 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 CA [auth B] SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] 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 CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] 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 CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], 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 CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Z [auth B]
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain MA [auth B]	MA [auth B] NA [auth B] P [auth A] PA [auth B] QA [auth B] MA [auth B], NA [auth B], P [auth A], PA [auth B], QA [auth B], R [auth A], S [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Focus chain NA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain MA [auth B] Focus chain NA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain R [auth A] Focus chain S [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain Q [auth A] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain T [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain T [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain T [auth A]	OA [auth B] Q [auth A] RA [auth B] SA [auth B] T [auth A] OA [auth B], Q [auth A], RA [auth B], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], X [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain OA [auth B] Focus chain Q [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain OA [auth B] Focus chain Q [auth A] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain X [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain N [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain N [auth A]	KA [auth B], N [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain KA [auth B] Focus chain N [auth A] Interactions & Density Focus chain KA [auth B] Focus chain N [auth A]
NO2 Query on NO2 Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain K [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain K [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain K [auth A]	HA [auth B], K [auth A]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain HA [auth B] Focus chain K [auth A] Interactions & Density Focus chain HA [auth B] Focus chain K [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain O [auth A]	IA [auth B] JA [auth B] L [auth A] LA [auth B] M [auth A] IA [auth B], JA [auth B], L [auth A], LA [auth B], M [auth A], O [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain O [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain O [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.154 (Depositor), 0.164 (DCC)
R-Value Work: 0.139 (Depositor), 0.151 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 192.529	α = 90
b = 192.529	β = 90
c = 192.529	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2023-09-06
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary