4GIS

crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, glycerol and dicarboxylates bound (mixed loops, space group I4122)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an enolase family member from vibrio harveyi (efi-target 501692) with homology to mannonate dehydratase, with mg, glycerol and dicarboxylates bound (mixed loops, space group I4122)

Vetting, M.W.Toro, R.Bhosle, R.Al Obaidi, N.F.Morisco, L.L.Wasserman, S.R.Sojitra, S.Washington, E.Scott Glenn, A.Chowdhury, S.Evans, B.Hammonds, J.Hillerich, B.Love, J.Seidel, R.D.Imker, H.J.Gerlt, J.A.Almo, S.C.Enzyme Function Initiative (EFI)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Enolase
A, B
422Vibrio harveyi 1DA3Mutation(s): 0 
Gene Names: VME_00770
UniProt
Find proteins for D0X4R4 (Vibrio harveyi (strain 1DA3))
Explore D0X4R4 
Go to UniProtKB:  D0X4R4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0X4R4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAE
Query on MAE

Download Ideal Coordinates CCD File 
M [auth B]MALEIC ACID
C4 H4 O4
VZCYOOQTPOCHFL-UPHRSURJSA-N
MLA
Query on MLA

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E [auth A]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL
Query on GOL

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D [auth A],
F [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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C [auth A],
H [auth A],
I [auth A],
J [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.152 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.195α = 90
b = 181.195β = 90
c = 115.835γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Non-polymer description
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description