4JD5

Crystal Structure of Benzoylformate Decarboxylase Mutant L403E

Structural Biology Knowledgebase: 4JD5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.134

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4JD5

Classification: LYASE

Total Structure Weight: 58220.12

Macromolecule Entities
Molecule Chains Length Organism Details
Benzoylformate decarboxylase A 536 Pseudomonas putida EC#: 4.1.1.7 IUBMB
Mutation: L403E
Gene Name(s): mdlC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]- 4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5- YL}ETHYL TRIHYDROGEN DIPHOSPHATE
THIAMIN THIAZOLONE DIPHOSPHATE (Synonym)
C12 H18 N4 O8 P2 S
ZGJUYGIRPQSCFA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.134
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.55 α = 90.00
b = 95.79 β = 90.00
c = 137.15 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-02-23
  • Released Date: 2013-05-22
  • Deposition author(s): Novak, W.R.P., Andrews, F.H., Tom, A.R., Gunderman, P.R., McLeish, M.J.

Revision History

No revisions since initial release