3T6C

Crystal structure of an enolase from pantoea ananatis (efi target efi-501676) with bound d-gluconate and mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of an enolase from pantoea ananatis (efi target efi-501676) with bound d-gluconate and 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
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ManD family dehydrataseA, B440Pantoea ananatis LMG 20103Mutation(s): 0 
Gene Names: rspAPANA_0592
EC: 4.2.1 (PDB Primary Data), 4.2.1.39 (UniProt)
UniProt
Find proteins for D4GJ14 (Pantoea ananatis (strain LMG 20103))
Explore D4GJ14 
Go to UniProtKB:  D4GJ14
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD4GJ14
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GCO
Query on GCO

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
D-gluconic acid
C6 H12 O7
RGHNJXZEOKUKBD-SQOUGZDYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
J [auth A],
R [auth B]
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.79α = 90
b = 130.79β = 90
c = 104.68γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Structure summary
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Database references, Derived calculations, Structure summary