3TTE

Crystal structure of enolase brado_4202 (target EFI-501651) from Bradyrhizobium complexed with magnesium and mandelic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Mandelate Racemase from Bradyrhizobium Sp. Ors278

Patskovsky, Y.Kim, J.Toro, R.Bhosle, R.Hillerich, B.Seidel, R.D.Washington, E.Scott Glenn, A.Chowdhury, S.Evans, B.Hammond, J.Zencheck, W.D.Imker, H.J.Gerlt, J.A.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mandelate racemase/muconate lactonizing enzyme
A, B
383Bradyrhizobium sp. ORS 278Mutation(s): 0 
Gene Names: BRADO4202
EC: 5.1.2.2 (PDB Primary Data), 5.5.1.1 (PDB Primary Data)
UniProt
Find proteins for A4YVM8 (Bradyrhizobium sp. (strain ORS 278))
Explore A4YVM8 
Go to UniProtKB:  A4YVM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4YVM8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SMN
Query on SMN

Download Ideal Coordinates CCD File 
D [auth A](S)-MANDELIC ACID
C8 H8 O3
IWYDHOAUDWTVEP-ZETCQYMHSA-N
GOL
Query on GOL

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E [auth A],
F [auth A],
H [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT
Query on FMT

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I [auth B]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
MG
Query on MG

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C [auth A],
G [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.949α = 90
b = 118.867β = 90
c = 130.571γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2012-02-22
    Changes: Database references, Structure summary
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description