1DIO

DIOL DEHYDRATASE-CYANOCOBALAMIN COMPLEX FROM KLEBSIELLA OXYTOCA

Structural Biology Knowledgebase: 1DIO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 1DIO

Classification: LYASE

Total Structure Weight: 210389.94

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (DIOL DEHYDRATASE) A, L 554 Klebsiella oxytoca EC#: 4.2.1.28 IUBMB
Gene Name(s): pddA pduC AB185_12495 SK88_04876 SK91_02751
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (DIOL DEHYDRATASE) B, E 224 Klebsiella oxytoca EC#: 4.2.1.28 IUBMB
Gene Name(s): pddB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PROTEIN (DIOL DEHYDRATASE) G, M 173 Klebsiella oxytoca EC#: 4.2.1.28 IUBMB
Gene Name(s): pddC pduE AB185_12485 KOJKO3_c4550 SK91_02753
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B12
Query on B12

B, E COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGO
Query on PGO

A, L S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, L POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.187
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 76.20 α = 90.00
b = 122.30 β = 90.00
c = 209.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-01-27
  • Released Date: 2000-01-30
  • Deposition author(s): Shibata, N., Masuda, J., Tobimatsu, T., Toraya, T., Suto, K., Morimoto, Y., Yasuoka, N.

Revision History

  • 2012-10-24
    Type: Non-polymer description | Details: --
  • 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