4E8G

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.

Kumar, R.Zhao, S.Vetting, M.W.Wood, B.M.Sakai, A.Cho, K.Solbiati, J.Almo, S.C.Sweedler, J.V.Jacobson, M.P.Gerlt, J.A.Cronan, J.E.

(2014) MBio 5: e00933-e00913


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein
A, B
391Paracoccus denitrificans (strain Pd 1222)Mutation(s): 0 
Gene Names: hpbD
EC: 5.1.1.22
Find proteins for A1B198 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B198
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.163 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 117.963α = 90.00
b = 117.963β = 90.00
c = 111.154γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
MOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Database references