2NAP

DISSIMILATORY NITRATE REDUCTASE (NAP) FROM DESULFOVIBRIO DESULFURICANS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods.

Dias, J.M.Than, M.E.Humm, A.Huber, R.Bourenkov, G.P.Bartunik, H.D.Bursakov, S.Calvete, J.Caldeira, J.Carneiro, C.Moura, J.J.Moura, I.Romao, M.J.

(1999) Structure Fold.Des. 7: 65-79

  • Also Cited By: 1OGY

  • PubMed Abstract: 
  • The periplasmic nitrate reductase (NAP) from the sulphate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. NAP is a molybdenum-containing enzy ...

    The periplasmic nitrate reductase (NAP) from the sulphate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. NAP is a molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide (MGD) cofactor and one [4Fe-4S] cluster in a single polypeptide chain of 723 amino acid residues. To date, there is no crystal structure of a nitrate reductase.


    Organizational Affiliation

    Departamento de Quimica, CQFB, FCT, Universidade Nova de Lisboa, Caparica, Portugal.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PERIPLASMIC NITRATE REDUCTASE)
A
723Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949)Gene Names: napA (nap)
EC: 1.7.99.4
Find proteins for P81186 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949))
Go to UniProtKB:  P81186
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
MO
Query on MO

Download SDF File 
Download CCD File 
A
MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
 Ligand Interaction
MGD
Query on MGD

Download SDF File 
Download CCD File 
A
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.260α = 90.00
b = 106.260β = 90.00
c = 134.910γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4model building
SHARPphasing
SCALEPACKdata scaling
CCP4phasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance