1SIW

Crystal structure of the apomolybdo-NarGHI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.244 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PHClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

The catalytic subunit of Escherichia coli nitrate reductase A contains a novel [4Fe-4S] cluster with a high-spin ground state

Rothery, R.A.Bertero, M.G.Cammack, R.Palak, M.Blasco, F.Strynadka, N.C.Weiner, J.H.

(2004) Biochemistry 43: 5324-5333

  • DOI: https://doi.org/10.1021/bi049938l
  • Primary Citation of Related Structures:  
    1SIW

  • PubMed Abstract: 

    We have used EPR spectroscopy, redox potentiometry, and protein crystallography to characterize the [4Fe-4S] cluster (FS0) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). FS0 is clearly visible in the crystal structure of NarGHI [Bertero, M. G., et al. (2003) Nat. Struct. Biol. 10, 681-687] but has novel coordination comprising one His residue and three Cys residues. At low temperatures (<15 K), reduced NarGHI exhibits a previously unobserved EPR signal comprising peaks at g = 5.023 and g = 5.556. We have assigned these features to a [4Fe-4S](+) cluster with an S = (3)/(2) ground state, with the g = 5.023 and g = 5.556 peaks corresponding to subpopulations exhibiting DeltaS = (1)/(2) and DeltaS = (3)/(2) transitions, respectively. Both peaks exhibit midpoint potentials of approximately -55 mV at pH 8.0 and are eliminated in the EPR spectrum of apomolybdo-NarGHI. The structure of apomolybdo-NarGHI reveals that FS0 is still present but that there is significant conformational disorder in a segment of residues that includes one of the Cys ligands. On the basis of these observations, we have assigned the high-spin EPR features of reduced NarGHI to FS0.


  • Organizational Affiliation

    CIHR Membrane Protein Research Group, Department of Biochemistry, University of Alberta, 474 Medical Sciences Building, Edmonton, Alberta T6G 2H7, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 alpha chain1,246Escherichia coliMutation(s): 0 
Gene Names: Operon narGHJI: NARGNARCBISDB1224
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P09152 (Escherichia coli (strain K12))
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Go to UniProtKB:  P09152
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09152
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 beta chain512Escherichia coliMutation(s): 0 
Gene Names: Operon narGHJI: NARHB1225
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P11349 (Escherichia coli (strain K12))
Explore P11349 
Go to UniProtKB:  P11349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11349
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 gamma chain225Escherichia coliMutation(s): 1 
Gene Names: Operon narGHJI: NARICHLIB1227
EC: 1.7.99.4 (PDB Primary Data), 1.7.5.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P11350 (Escherichia coli (strain K12))
Explore P11350 
Go to UniProtKB:  P11350
Entity Groups  
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UniProt GroupP11350
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PH
Query on 3PH

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
HEM
Query on HEM

Download Ideal Coordinates CCD File 
L [auth C],
M [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth B],
I [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

Download Ideal Coordinates CCD File 
J [auth B]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
C
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.244 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.001α = 90
b = 241.282β = 90
c = 140.387γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 3PHClick on this verticalbar to view detailsBest fitted HEMClick on this verticalbar to view detailsBest fitted GDPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-12-21
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary