4H2H

Crystal structure of an enolase (mandalate racemase subgroup, target EFI-502101) from Pelagibaca bermudensis htcc2601, with bound mg and l-4-hydroxyproline betaine (betonicine)

Structural Biology Knowledgebase: 4H2H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.159

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4H2H

Classification: ISOMERASE

Total Structure Weight: 335293.05

Macromolecule Entities
Molecule Chains Length Organism Details
Mandelate racemase/muconate lactonizing enzyme A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 376 Pelagibaca bermudensis EC#: 5.1.1 IUBMB
Gene Name(s): hpbD R2601_01638

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0XW
Query on 0XW

A, B, C, D, E, F, G, H (2S,4R)-4-hydroxy-1,1-dimethylpyrrolidinium- 2-carboxylate
Betonicine, L-4-Hydroxyproline betaine (Synonym)
C7 H13 N O3
MUNWAHDYFVYIKH-RITPCOANSA-N
Ligand Explorer
 
JSmol
IOD
Query on IOD

A, B, C, D, E, F, G, H IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
MG
Query on MG

A, B, C, D, E, F, G, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MPD
Query on MPD

C, D, E (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
JSmol
NI
Query on NI

A, B NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.159
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.04 α = 90.00
b = 152.82 β = 105.20
c = 113.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-09-12
  • Released Date: 2012-10-10
  • Deposition author(s): Vetting, M.W., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History

  • 2013-11-06
    Type: Citation | Details: Citation update
  • 2013-09-18
    Type: Citation | Details: --