1QDB

CYTOCHROME C NITRITE REDUCTASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of cytochrome c nitrite reductase.

Einsle, O.Messerschmidt, A.Stach, P.Bourenkov, G.P.Bartunik, H.D.Huber, R.Kroneck, P.M.

(1999) Nature 400: 476-480

  • DOI: 10.1038/22802
  • Primary Citation of Related Structures:  
    1QDB

  • PubMed Abstract: 
  • The enzyme cytochrome c nitrite reductase catalyses the six-electron reduction of nitrite to ammonia as one of the key steps in the biological nitrogen cycle, where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification ...

    The enzyme cytochrome c nitrite reductase catalyses the six-electron reduction of nitrite to ammonia as one of the key steps in the biological nitrogen cycle, where it participates in the anaerobic energy metabolism of dissimilatory nitrate ammonification. Here we report on the crystal structure of this enzyme from the microorganism Sulfurospirillum deleyianum, which we solved by multiwavelength anomalous dispersion methods. We propose a reaction scheme for the transformation of nitrite based on structural and spectroscopic information. Cytochrome c nitrite reductase is a functional dimer, with 10 close-packed haem groups of type c and an unusual lysine-coordinated high-spin haem at the active site. By comparing the haem arrangement of this nitrite reductase with that of other multihaem cytochromes, we have been able to identify a family of proteins in which the orientation of haem groups is conserved whereas structure and function are not.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Martinsried, Germany. einsle@biochem.mpg.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME C NITRITE REDUCTASEA, B, C473Sulfurospirillum deleyianumMutation(s): 0 
Gene Names: nrfA
EC: 1.7.2.2
UniProt
Find proteins for Q9Z4P4 (Sulfurospirillum deleyianum)
Explore Q9Z4P4 
Go to UniProtKB:  Q9Z4P4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , H [auth A] , I [auth A] , J [auth A] , K [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  H [auth A],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  Q [auth B],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  Z [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , N [auth B] , O [auth B] , P [auth B] , W [auth C] , X [auth C] , 
E [auth A],  F [auth A],  G [auth A],  N [auth B],  O [auth B],  P [auth B],  W [auth C],  X [auth C],  Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A], M [auth B], V [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.484α = 90
b = 185.344β = 90
c = 92.192γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2021-03-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary