3TFN | pdb_00003tfn

Crystal structure of dehydrosqualene synthase (crtm) from s. aureus complexed with bph-1183

• PDB DOI: https://doi.org/10.2210/pdb3TFN/pdb

• Classification: TRANSFERASE/transferase inhibitor
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-08-16 Released: 2012-04-04 
• Deposition Author(s): Lin, F.-Y., Liu, Y.-L., Oldfield, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Dual dehydrosqualene/squalene synthase inhibitors: leads for innate immune system-based therapeutics.

Lin, F.Y., Zhang, Y., Hensler, M., Liu, Y.L., Chow, O.A., Zhu, W., Wang, K., Pang, R., Thienphrapa, W., Nizet, V., Oldfield, E.

(2012) ChemMedChem 7: 561-564

• PubMed: 22290830 
• DOI: https://doi.org/10.1002/cmdc.201100589
• Primary Citation Related Structures: 
  3TFN, 3TFP, 3TFV

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Organizational Affiliation: 
• Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 35.23 kDa 
• Atom Count: 2,609 
• Modeled Residue Count: 284 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrosqualene synthase	A	293	Staphylococcus aureus	Mutation(s): 0  Gene Names: crtM EC: 2.5.1 (PDB Primary Data), 2.5.1.96 (UniProt)
UniProt
Find proteins for A9JQL9 (Staphylococcus aureus) Explore A9JQL9  Go to UniProtKB:  A9JQL9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2CJ	B [auth A]	(1-{2-[4-(diphenylmethyl)piperazin-1-yl]-2-oxoethyl}cyclopentyl)acetic acid C26 H32 N2 O3 GLJDWAQYHLAMPV-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.229	α = 90
b = 80.229	β = 90
c = 91.82	γ = 120

Software Package:

Software Name	Purpose
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Lin, F.-Y., Liu, Y.-L., Oldfield, E.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2012-05-23
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description