3F29 | pdb_00003f29

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

PDB DOI: https://doi.org/10.2210/pdb3F29/pdb

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

Deposited: 2008-10-29 Released: 2008-12-09
Deposition Author(s): Trofimov, A.A., Polyakov, K.M., Boyko, K.M., Slutsky, A., Tikhonova, T.V., Antipov, A.N., Zvyagilskaya, R.A., Popov, A.N., Lamzin, V.S., Bourenkov, G.P., Popov, V.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.174 (Depositor)
R-Value Work:
0.154 (Depositor), 0.157 (DCC)
R-Value Observed:
0.155 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 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: 132.21 kDa
Atom Count: 10,215
Modeled Residue Count: 1,039
Deposited Residue Count: 1,050
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [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]
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain N [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain N [auth A]	GA [auth B], HA [auth B], N [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain N [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain N [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain MA [auth B] SDF format, chain LA [auth B] SDF format, chain KA [auth B] SDF format, chain JA [auth B] SDF format, chain IA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B]	IA [auth B] JA [auth B] KA [auth B] LA [auth B] MA [auth B] IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
SO3 Query on SO3 Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain FA [auth B] SDF format, chain CA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain CA [auth B]	CA [auth B], FA [auth B], K [auth A]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain FA [auth B] Focus chain K [auth A] Interactions & Density Focus chain CA [auth B] Focus chain FA [auth B] Focus chain K [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B]	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: 2.00 Å
R-Value Free: 0.174 (Depositor)
R-Value Work: 0.154 (Depositor), 0.157 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.568	α = 90
b = 193.568	β = 90
c = 193.568	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-12-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-12-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-10-22
Changes: Derived calculations
Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.4: 2024-11-06
Changes: Structure summary