3MMO

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

Starting Model: experimental
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This is version 1.4 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 D Biol Crystallogr 66: 1043-1047

  • DOI: https://doi.org/10.1107/S0907444910031665
  • Primary Citation of Related Structures:  
    3FO3, 3MMO

  • 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) = 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Eight-heme nitrite reductase
A, B
525Thioalkalivibrio nitratireducensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0DSL2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
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],
H [auth A],
I [auth A],
J [auth A],
Y [auth B],
Z [auth B]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PG6
Query on PG6

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JA [auth B],
N [auth A],
R [auth A]
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PG4
Query on PG4

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KA [auth B]
LA [auth B]
MA [auth B]
NA [auth B]
O [auth A]
KA [auth B],
LA [auth B],
MA [auth B],
NA [auth B],
O [auth A],
OA [auth B],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
TRS
Query on TRS

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U [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
CA
Query on CA

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HA [auth B],
IA [auth B],
L [auth A],
M [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CYN
Query on CYN

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GA [auth B],
K [auth A]
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
NA
Query on NA

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UA [auth B]
V [auth A]
VA [auth B]
W [auth A]
WA [auth B]
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
WA [auth B],
X [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.56α = 90
b = 194.56β = 90
c = 194.56γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-03-28
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-27
    Changes: Structure summary