4IZG

Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound cis-4oh-d-proline betaine (product)

Structural Biology Knowledgebase: 4IZG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.165

Literature

Macromolecules
Sequence Display for 4IZG

Classification: ISOMERASE

Total Structure Weight: 87838.54

Macromolecule Entities
Molecule Chains Length Organism Details
Mandelate racemase/muconate lactonizing enzyme, N-terminal domain protein A, B 391 Paracoccus denitrificans EC#: 5.1.1 IUBMB
Gene Name(s): hpbD Pden_1187
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4OP
Query on 4OP

A, B (2S,4S)-2-carboxy-4-hydroxy-1,1-dimethylpyrrolidinium
CIS-4OH-D-PROLINE BETAINE (Synonym)
C7 H14 N O3
MUNWAHDYFVYIKH-PHDIDXHHSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

A, B IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197
  • R-Value Work: 0.165
  • Space Group: P 4 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 117.46 α = 90.00
b = 117.46 β = 90.00
c = 111.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-01-29
  • Released Date: 2013-02-13
  • Deposition author(s): Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala, S., Kar, A., LaFleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History

No revisions since initial release