1YNO

High Resolution Structure of Benzoylformate Decarboxylase from Pseudomonas Putida Complexed with Thiamine Thiazolone Diphosphate

Structural Biology Knowledgebase: 1YNO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.155
  • R-Value Work: 0.124

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YNO

Classification: LYASE

Total Structure Weight: 56857.05

Macromolecule Entities
Molecule Chains Length Organism Details
Benzoylformate decarboxylase A 527 Pseudomonas putida EC#: 4.1.1.7 IUBMB
Gene Name(s): mdlC

Small Molecules
Ligands 3 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)
CA
Query on CA

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.155
  • R-Value Work: 0.124
  • Space Group: I 2 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 80.95 α = 90.00
b = 95.46 β = 90.00
c = 136.70 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-24
  • Released Date: 2006-01-17
  • Deposition author(s): Bera, A.K., Hasson, M.S.

Revision History

  • 2011-07-13
    Type: Atom occupancy | Details: Restore author's atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values