1OGY

Crystal structure of the heterodimeric nitrate reductase from Rhodobacter sphaeroides


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural and Redox Plasticity in the Heterodimeric Periplasmic Nitrate Reductase

Arnoux, P.Sabaty, M.Alric, J.Frangioni, B.Guigliarelli, B.Adriano, J.-M.Pignol, D.

(2003) Nat Struct Biol 10: 928

  • DOI: https://doi.org/10.1038/nsb994
  • Primary Citation of Related Structures:  
    1OGY

  • PubMed Abstract: 

    The structure of the respiratory nitrate reductase (NapAB) from Rhodobacter sphaeroides, the periplasmic heterodimeric enzyme responsible for the first step in the denitrification process, has been determined at a resolution of 3.2 A. The di-heme electron transfer small subunit NapB binds to the large subunit with heme II in close proximity to the [4Fe-4S] cluster of NapA. A total of 57 residues at the N- and C-terminal extremities of NapB adopt an extended conformation, embracing the NapA subunit and largely contributing to the total area of 5,900 A(2) buried in the complex. Complex formation was studied further by measuring the variation of the redox potentials of all the cofactors upon binding. The marked effects observed are interpreted in light of the three-dimensional structure and depict a plasticity that contributes to an efficient electron transfer in the complex from the heme I of NapB to the molybdenum catalytic site of NapA.


  • Organizational Affiliation

    CEA/Cadarache, DSV, DEVM, Laboratoire de Bioénergétique Cellulaire, 13108 St Paul lez Durance Cedex, France. pascal.arnoux@cea.fr


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PERIPLASMIC NITRATE REDUCTASE
A, C, E, G, I
A, C, E, G, I, K, M, O
802Cereibacter sphaeroidesMutation(s): 0 
EC: 1.7.99.4
UniProt
Find proteins for Q53176 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q53176 
Go to UniProtKB:  Q53176
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53176
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DIHEME CYTOCHROME C NAPB MOLECULE: NITRATE REDUCTASE
B, D, F, H, J
B, D, F, H, J, L, N, P
130Cereibacter sphaeroidesMutation(s): 0 
UniProt
Find proteins for Q53177 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q53177 
Go to UniProtKB:  Q53177
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53177
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
CB [auth M]
DB [auth M]
EA [auth E]
FA [auth E]
IB [auth O]
CB [auth M],
DB [auth M],
EA [auth E],
FA [auth E],
IB [auth O],
JB [auth O],
KA [auth G],
LA [auth G],
QA [auth I],
RA [auth I],
S [auth A],
T [auth A],
WA [auth K],
XA [auth K],
Y [auth C],
Z [auth C]
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
EB [auth N]
FB [auth N]
GA [auth F]
AA [auth D],
BA [auth D],
EB [auth N],
FB [auth N],
GA [auth F],
HA [auth F],
KB [auth P],
LB [auth P],
MA [auth H],
NA [auth H],
SA [auth J],
TA [auth J],
U [auth B],
V [auth B],
YA [auth L],
ZA [auth L]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AB [auth M]
CA [auth E]
GB [auth O]
IA [auth G]
OA [auth I]
AB [auth M],
CA [auth E],
GB [auth O],
IA [auth G],
OA [auth I],
Q [auth A],
UA [auth K],
W [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
MO
Query on MO

Download Ideal Coordinates CCD File 
BB [auth M]
DA [auth E]
HB [auth O]
JA [auth G]
PA [auth I]
BB [auth M],
DA [auth E],
HB [auth O],
JA [auth G],
PA [auth I],
R [auth A],
VA [auth K],
X [auth C]
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123α = 90
b = 225.2β = 92.1
c = 154.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-16
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description