6CO9

Crystal structure of Rhodococcus jostii RHA1 IpdAB COCHEA-COA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.602 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

IpdAB, a virulence factor inMycobacterium tuberculosis, is a cholesterol ring-cleaving hydrolase.

Crowe, A.M.Workman, S.D.Watanabe, N.Worrall, L.J.Strynadka, N.C.J.Eltis, L.D.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E3378-E3387


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable CoA-transferase alpha subunit
A
308Rhodococcus jostii (strain RHA1)Mutation(s): 0 
Find proteins for Q0S7P9 (Rhodococcus jostii (strain RHA1))
Go to UniProtKB:  Q0S7P9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Probable CoA-transferase beta subunit
B
253Rhodococcus jostii (strain RHA1)Mutation(s): 0 
Find proteins for Q0S7Q0 (Rhodococcus jostii (strain RHA1))
Go to UniProtKB:  Q0S7Q0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F8G
Query on F8G

Download SDF File 
Download CCD File 
B
S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (5R,10R)-7-hydroxy-10-methyl-2-oxo-1-oxaspiro[4.5]dec-6-ene-6-carbothioate (non-preferred name)
C32 H48 N7 O20 P3 S
COMHLEMSBYWTLA-LJKJHTHQSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.602 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.161 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.294α = 90.00
b = 69.294β = 90.00
c = 241.855γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references
  • Version 1.3: 2018-06-13
    Type: Data collection, Structure summary