3EGW

The crystal structure of the NarGHI mutant NarH - C16A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

When width is more important than height: Barriers to electron transfer in E.coli nitrate reductase

Parkin, A.Blanford, C.F.Rothery, R.A.Macey, R.Bertero, M.Strynadka, N.C.J.Armstrong, F.A.Weiner, J.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 alpha chainA1,244Escherichia coli K-12Mutation(s): 0 
Gene Names: narGbisDnarCb1224JW1215
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))
Explore P09152 
Go to UniProtKB:  P09152
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09152
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 beta chainB509Escherichia coli K-12Mutation(s): 1 
Gene Names: narHb1225JW1216
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Respiratory nitrate reductase 1 gamma chainC225Escherichia coli K-12Mutation(s): 0 
Gene Names: narIchlIb1227JW1218
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  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11350
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
E [auth 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
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
MD1
Query on MD1

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D [auth A]PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER
C20 H26 N10 O13 P2 S2
IRGDLSAXQOKWLX-XHEYTWMPSA-N
 Ligand Interaction
3PH
Query on 3PH

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L [auth B]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
 Ligand Interaction
HEM
Query on HEM

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M [auth C],
N [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
AGA
Query on AGA

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O [auth C](1S)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTANOYLOXY)METHYL]ETHYL OCTANOATE
C19 H36 O10 P
UQSXQYRZHMGKIE-DLBZAZTESA-M
 Ligand Interaction
SF4
Query on SF4

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G [auth A],
I [auth B],
J [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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H [auth B],
K [auth B]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
6MO
Query on 6MO

Download Ideal Coordinates CCD File 
F [auth A]MOLYBDENUM(VI) ION
Mo
HCNGUXXTNNIKCQ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
C L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.995α = 90
b = 241.684β = 90
c = 139.475γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations