1XDS

Crystal structure of Aclacinomycin-10-hydroxylase (RdmB) in complex with S-adenosyl-L-methionine (SAM) and 11-deoxy-beta-rhodomycin (DbrA)

Structural Biology Knowledgebase: 1XDS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.251

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XDS

Classification: transferase

Total Structure Weight: 82669.80

Macromolecule Entities
Molecule Chains Length Organism Details
Protein RdmB A, B 374 Streptomyces purpurascens EC#: 4.1.1 IUBMB
Mutation: M1M, M31M, M96M, M163M, M196M, M308M, M312M
Gene Name(s): rdmB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 11-DEOXY-BETA-RHODOMYCIN
C40 H51 N O14
OQDCVONZQOVIMP-UNQJTBPASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SAM
Query on SAM

A, B S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-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, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.296
  • R-Value Work: 0.251
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 79.89 α = 90.00
b = 79.89 β = 90.00
c = 232.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-09-08
  • Released Date: 2004-11-23
  • Deposition author(s): Jansson, A., Koskiniemi, H., Erola, A., Wang, J., Mantsala, P., Schneider, G., Niemi, J., Structural Proteomics in Europe (SPINE)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4