9KP1 | pdb_00009kp1

Heterodimer of heptaprenyl diphosphate synthase from B. subtilis

• PDB DOI: https://doi.org/10.2210/pdb9KP1/pdb

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


• Deposited: 2024-11-22 Released: 2025-11-26 
• Deposition Author(s): Luo, S., Liu, Z.C., Wang, G.G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Models: experimental

Literature

Structural insight into heptaprenyl diphosphate synthase from B. subtilis

Luo, S., Liu, Z.C., Wang, G.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 69.99 kDa 
• Atom Count: 4,366 
• Modeled Residue Count: 544 
• Deposited Residue Count: 609 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heptaprenyl diphosphate synthase component 1	A	261	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: hepS, gerC1, gerCA, hepA, BSU22760 EC: 2.5.1.30
UniProt
Find proteins for P31112 (Bacillus subtilis (strain 168)) Explore P31112  Go to UniProtKB:  P31112

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heptaprenyl diphosphate synthase component 2	B	348	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: hepT, gerC3, gerCC, hepB, BSU22740 EC: 2.5.1.30
UniProt
Find proteins for P31114 (Bacillus subtilis (strain 168)) Explore P31114  Go to UniProtKB:  P31114

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.260 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.865	α = 90
b = 145.199	β = 90
c = 124.736	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Luo, S., Liu, Z.C., Wang, G.G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release