3VZX

Crystal structure of PcrB from bacillus subtilis subap. subtilis str. 168


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus

Ren, F.Feng, X.Ko, T.P.Huang, C.H.Hu, Y.Chan, H.C.Liu, Y.L.Wang, K.Chen, C.C.Pang, X.He, M.Li, Y.Oldfield, E.Guo, R.T.

(2013) Chembiochem 14: 195-199

  • DOI: 10.1002/cbic.201200748
  • Primary Citation of Related Structures:  
    3W00, 3W01, 3W02, 3VZX, 3VZY, 3VZZ

  • PubMed Abstract: 
  • Well structured: As a new triose phosphate isomerase (TIM) barrel-fold prenyl transferase, PcrB catalyzes the production of heptaprenylglyceryl phosphate from heptaprenyl diphosphate and glycerol-1-phosphate. Crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus in complex with ligands were solved, and together with site-directed mutagenesis and bioinformatics analyses, clearly reveal the catalytic mechanism of the enzyme ...

    Well structured: As a new triose phosphate isomerase (TIM) barrel-fold prenyl transferase, PcrB catalyzes the production of heptaprenylglyceryl phosphate from heptaprenyl diphosphate and glycerol-1-phosphate. Crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus in complex with ligands were solved, and together with site-directed mutagenesis and bioinformatics analyses, clearly reveal the catalytic mechanism of the enzyme.


    Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin 300308, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heptaprenylglyceryl phosphate synthaseA, B228Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: pcrByerEBSU06600
EC: 2.5.1
Find proteins for O34790 (Bacillus subtilis (strain 168))
Explore O34790 
Go to UniProtKB:  O34790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , H [auth A] , M [auth B] , N [auth B] , 
C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  H [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.116α = 90
b = 55.953β = 108.46
c = 77.271γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references