3TOY

CRYSTAL STRUCTURE OF ENOLASE BRADO_4202 (TARGET EFI-501651) FROM Bradyrhizobium sp. ORS278 WITH CALCIUM AND ACETATE BOUND


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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 family protein
A, B, C, D
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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P4C
Query on P4C

Download Ideal Coordinates CCD File 
H [auth A]
M [auth B]
N [auth B]
R [auth C]
S [auth C]
H [auth A],
M [auth B],
N [auth B],
R [auth C],
S [auth C],
X [auth D]
O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL
C14 H28 O8
CTLLATPOKUEFSQ-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
Q [auth C],
V [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI
Query on NI

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
W [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
I [auth A]
J [auth B]
O [auth B]
P [auth C]
E [auth A],
I [auth A],
J [auth B],
O [auth B],
P [auth C],
T [auth C],
U [auth D],
Y [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.389α = 90
b = 131.838β = 90
c = 108.825γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-21
    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