4DI8

CRYSTAL STRUCTURE OF THE D248A mutant of 2-PYRONE-4,6-DICARBOXYLIC ACID HYDROLASE FROM SPHINGOMONAS PAUCIMOBILIS complexed with substrate at pH 8.5

Structural Biology Knowledgebase: 4DI8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.157

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DI8

Classification: HYDROLASE

Total Structure Weight: 68913.23

Macromolecule Entities
Molecule Chains Length Organism Details
2-pyrone-4,6-dicarbaxylate hydrolase A, B 303 Sphingomonas paucimobilis Mutation: D248A
Gene Name(s): ligI

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0GY
Query on 0GY

A, B (1E,3Z)-4-hydroxybuta-1,3-diene-1,2,4-tricarboxylic acid
C7 H6 O7
QWLUKZXOQAQUFQ-NAOWAUKJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
0GZ
Query on 0GZ

A, B 2-oxo-2H-pyran-4,6-dicarboxylic acid
C7 H4 O6
VRMXCPVFSJVVCA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.187
  • R-Value Work: 0.157
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 74.35 α = 90.00
b = 52.13 β = 93.73
c = 76.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-11
  • Released Date: 2012-10-03
  • Deposition author(s): Malashkevich, V.N., Toro, R., Hobbs, M.E., Raushel, F.M., Almo, S.C.
  • Previous versions: 4D95

Revision History

  • 2013-02-20
    Type: Citation | Details: Citation update
  • 2013-01-23
    Type: Citation | Details: Citation update
  • 2013-01-09
    Type: Citation | Details: Citation update