3RYK

1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) from Bacillus anthracis str. Ames with TDP and PPi bound

Structural Biology Knowledgebase: 3RYK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.160
  • R-Value Work: 0.123

Literature

Macromolecules
Sequence Display for 3RYK

Classification: ISOMERASE

Total Structure Weight: 47481.48

Macromolecule Entities
Molecule Chains Length Organism Details
dTDP-4-dehydrorhamnose 3,5-epimerase A, B 205 Bacillus anthracis EC#: 5.1.3.13 IUBMB
Gene Name(s): rfbC GBAA_1229 AB163_10470 AB164_10315 AB165_23785 AB166_26695 AB167_12550 AB168_03065 AB169_20220 AB170_18570 AB171_21290 AB893_06310 ABW01_04125 ADK17_07665 ADK18_06090 ADT20_17375 ADT21_06055 BASH2_04624 BF27_739
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A THYMIDINE-5'-DIPHOSPHATE
C10 H16 N2 O11 P2
UJLXYODCHAELLY-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
POP
Query on POP

A PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 86.65 α = 90.00
b = 86.65 β = 90.00
c = 45.10 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-11
  • Released Date: 2011-05-25
  • Deposition author(s): Halavaty, A.S., Kuhn, M., Minasov, G., Shuvalova, L., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

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