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

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 9KP1

This is version 1.0 of the entry. See complete history.

Literature

Structural insight into heptaprenyl diphosphate synthase from B. subtilis

Luo, S., Liu, Z.C., Wang, G.G.

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31112
Sequence Annotations Expand
Reference Sequence

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31114
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.