3THU

Crystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg

Vetting, M.W.Toro, R.Bhosle, R.Wasserman, S.R.Morisco, L.L.Hillerich, B.Washington, E.Scott Glenn, A.Chowdhury, S.Evans, B.Hammonds, J.Zencheck, W.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
Mandelate racemase / muconate lactonizing enzyme family protein
A, B, C
426Sphingomonas sp. SKA58Mutation(s): 0 
Gene Names: SKA58_08619
UniProt
Find proteins for Q1NAJ2 (Sphingomonas sp. (strain SKA58))
Explore Q1NAJ2 
Go to UniProtKB:  Q1NAJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1NAJ2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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F [auth A]
G [auth A]
L [auth B]
M [auth B]
N [auth B]
F [auth A],
G [auth A],
L [auth B],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
T [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

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E [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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D [auth A],
J [auth B],
Q [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
O [auth B]
P [auth B]
U [auth C]
H [auth A],
I [auth A],
O [auth B],
P [auth B],
U [auth C],
V [auth C]
UNKNOWN ATOM OR ION
X
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.140 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.799α = 90
b = 124.799β = 90
c = 343.092γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASESphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Structure summary
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description