3FO3

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.126 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of complexes of octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens with sulfite and cyanide

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

(2010) Acta Crystallogr.,Sect.D 66: 1043-1047

  • DOI: 10.1107/S0907444910031665
  • Primary Citation of Related Structures:  
  • Also Cited By: 2OT4

  • PubMed Abstract: 
  • The structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 Å resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 Å resolution; R(cryst) ...

    The structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 Å resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 Å resolution; R(cryst) = 0.148) have been established. The complex with sulfite was prepared by the reduction of the protein crystal with sodium dithionite. The sulfite ion is bound to the iron ion of the catalytic haem through the S atom. The Fe-S distance is 2.24 Å. The structure of the cyanide complex with full occupancy of the ligand site was established for the first time for cytochrome c nitrite reductases. The cyanide ion is bound to the catalytic haem iron through the C atom. The Fe-C distance is 1.91 Å and the Fe-C-N angle is 171°. The sulfite reductase activity of TvNiR was measured at different pH values. The activity is 0.02 µmol of HS(-) per minute per milligram at pH 7.0; it decreases with increasing pH and is absent at pH 9.0.


    Organizational Affiliation

    Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia. kostya@eimb.ru




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Eight-heme nitrite reductase
A, B
525Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2)Mutation(s): 0 
Gene Names: nir
EC: 1.7.2.2
Find proteins for L0DSL2 (Thioalkalivibrio nitratireducens (strain DSM 14787 / UNIQEM 213 / ALEN2))
Go to UniProtKB:  L0DSL2
Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SO3
Query on SO3

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A, B
SULFITE ION
O3 S
LSNNMFCWUKXFEE-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
THJ
Query on THJ

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A, B
THIOSULFATE
O3 S2
DHCDFWKWKRSZHF-UHFFFAOYSA-L
 Ligand Interaction
HEC
Query on HEC

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A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
PG6
Query on PG6

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A, B
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.126 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 193.790α = 90.00
b = 193.790β = 90.00
c = 193.790γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance