3VZX | pdb_00003vzx

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

• PDB DOI: https://doi.org/10.2210/pdb3VZX/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-10-17 Released: 2012-12-26 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 

Starting Model: experimental

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

• PubMed: 23322418 
• DOI: https://doi.org/10.1002/cbic.201200748
• Primary Citation Related Structures: 
  3VZX, 3VZY, 3VZZ, 3W00, 3W01, 3W02


• 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.64 kDa 
• Atom Count: 4,051 
• Modeled Residue Count: 455 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heptaprenylglyceryl phosphate synthase	A, B	228	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: pcrB EC: 2.5.1
UniProt
Find proteins for O34790 (Bacillus subtilis (strain 168)) Explore O34790  Go to UniProtKB:  O34790

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	I [auth A], J [auth A], K [auth A], L [auth A], Q [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.225 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.116	α = 90
b = 55.953	β = 108.46
c = 77.271	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description