1MDO

Crystal structure of ArnB aminotransferase with pyridomine 5' phosphate

Structural Biology Knowledgebase: 1MDO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1MDO

Classification: Transferase

Total Structure Weight: 43690.08

Macromolecule Entities
Molecule Chains Length Organism Details
ArnB aminotransferase A 393 Salmonella enterica EC#: 2.6.1.87 IUBMB
Mutation: M1M, M6M, M7M, M18M, M67M, M72M, M87M, M95M, M105M, M114M, M277M, M316M, M367M
Gene Name(s): arnB pbgP pbgP1 pmrH STM2297

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

A 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
PYRIDOXAMINE-5'-PHOSPHATE (Synonym)
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.210
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.15 α = 90.00
b = 91.15 β = 90.00
c = 128.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-08-07
  • Released Date: 2002-12-11
  • Deposition author(s): Noland, B.W., Newman, J.M., Hendle, J., Badger, J., Christopher, J.A., Tresser, J., Buchanan, M.D., Wright, T., Rutter, M.E., Sanderson, W.E., Muller-Dieckmann, H.-J., Gajiwala, K., Buchanan, S.G.

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