4RM1

The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus DSM 20745


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.169

Literature

Macromolecules
Sequence Display for 4RM1

Classification: LYASE

Total Structure Weight: 213451.81

Macromolecule Entities
Molecule Chains Length Organism Details
Pyridoxal-dependent decarboxylase A, B, C, D 486 Sphaerobacter thermophilus EC#: 4.1.1.15 IUBMB
Mutation: Y333Q
Gene Name(s): Sthe_2364
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B, C 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE (Synonym)
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

B, D CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
LLP
Query on LLP
A, B, C, D L-PEPTIDE LINKING C14 H22 N3 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.169
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 69.55 α = 90.00
b = 125.00 β = 99.62
c = 132.24 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-10-18
  • Released Date: 2014-11-12
  • Deposition author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

No revisions since initial release