1YKM

Protocatechuate 3,4-Dioxygenase Y408E mutant

Structural Biology Knowledgebase: 1YKM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YKM

Classification: OXIDOREDUCTASE

Total Structure Weight: 294440.08

Macromolecule Entities
Molecule Chains Length Organism Details
Protocatechuate 3,4-dioxygenase alpha chain A, C, E..., G, I, KA, C, E, G, I, K 200 Pseudomonas putida EC#: 1.13.11.3 IUBMB
Gene Name(s): pcaG
Protocatechuate 3,4-dioxygenase beta chain B, D, F..., H, J, LB, D, F, H, J, L 238 Pseudomonas putida EC#: 1.13.11.3 IUBMB
Mutation: Y408E, C429X
Gene Name(s): pcaH

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

B, D, F, H, J, L FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
B, D, F, H, J, L L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.169
  • Space Group: I 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 196.61 α = 90.00
b = 127.73 β = 97.66
c = 134.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-01-18
  • Released Date: 2005-08-16
  • Deposition author(s): Brown, C.K., Ohlendorf, D.H.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4