7LBJ | pdb_00007lbj

Crystal structure of octaprenyl diphosphate synthase from Stenotrophomonas maltophilia

• PDB DOI: https://doi.org/10.2210/pdb7LBJ/pdb

• Classification: TRANSFERASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-08 Released: 2021-02-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of octaprenyl diphosphate synthase from Stenotrophomonas maltophilia

Bolejack, M.J., Abendroth, J.A., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 64.35 kDa 
• Atom Count: 4,611 
• Modeled Residue Count: 553 
• Deposited Residue Count: 600 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyltranstransferase	A, B	300	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: ispA, Smlt3467 EC: 2.5.1.10
UniProt
Find proteins for B2FP37 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FP37  Go to UniProtKB:  B2FP37

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.151 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.06	α = 90
b = 60.33	β = 90
c = 164.36	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2025-10-22
  Changes: Structure summary