2VYC

Crystal Structure of Acid Induced Arginine Decarboxylase from E. coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 2VYC

Classification: LYASE

Total Structure Weight: 847598.50

Macromolecule Entities
Molecule Chains Length Organism Details
BIODEGRADATIVE ARGININE DECARBOXYLASE A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 755 Escherichia coli EC#: 4.1.1.19 IUBMB
Details: COVELENT BOND BETWEEN COFACTOR PYRIDOXAL 5' PHOSPHATE (PLP) AND RESIDUE LYS386.
Gene Name(s): adiA adi b4117 JW5731
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PLP
Query on PLP

A, B, C, D, E, F, G, H, I, J PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.177
  • Space Group: P 64

Unit Cell:

Length (Å) Angle (°)
a = 197.65 α = 90.00
b = 197.65 β = 90.00
c = 450.32 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-22
  • Released Date: 2009-03-31
  • Deposition author(s): Andrell, J., Hicks, M.G., Palmer, T., Carpenter, E.P., Iwata, S., Maher, M.J.

Revision History

  • 2015-12-02
    Type: Other | Details: TER, MODRES, MASTER
  • 2015-12-02
    Type: Polymer description | Details: SEQRES
  • 2015-12-02
    Type: Data collection | Details: REMARK 200
  • 2015-12-02
    Type: Atom nomenclature | Details: ATOM, HETATM
  • 2015-12-02
    Type: Geometry validation | Details: REMARK 500
  • 2015-12-02
    Type: Refinement description | Details: REMARK 3
  • 2015-12-02
    Type: Linkage | Details: CONECT, LINK
  • 2015-12-02
    Type: Non-polymer description | Details: HETSYN, FORMUL, HETNAM, HET
  • 2015-12-02
    Type: Secondary structure | Details: SHEET
  • 2015-12-02
    Type: Binding sites and description | Details: REMARK 800, SITE
  • 2011-10-12
    Type: Citation | Details: JRNL
  • 2011-10-12
    Type: Other | Details: REMARK 375
  • 2011-10-12
    Type: Entry authorship | Details: AUTHOR
  • 2011-10-12
    Type: Biological assembly | Details: REMARK 350
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4