5IYS | pdb_00005iys

Crystal structure of a dehydrosqualene synthase in complex with ligand

• PDB DOI: https://doi.org/10.2210/pdb5IYS/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Enterococcus hirae ATCC 9790
• Mutation(s): No 


• Deposited: 2016-03-24 Released: 2017-03-29 
• Deposition Author(s): Liu, G.Z., Liu, W.D., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 
  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a dehydrosqualene synthase in complex with ligand

Liu, G.Z., Liu, W.D., Chen, C.C., Guo, R.T.

To be published.

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: 34.8 kDa 
• Atom Count: 2,589 
• Modeled Residue Count: 283 
• Deposited Residue Count: 289 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phytoene synthase	A	289	Enterococcus hirae ATCC 9790	Mutation(s): 0
UniProt
Find proteins for I6T9U8 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore I6T9U8  Go to UniProtKB:  I6T9U8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FPS	G [auth A], H [auth A]	S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE C15 H28 O6 P2 S MYMLCRQRXFRQGP-YFVJMOTDSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	D [auth A], E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free:  0.220 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.238	α = 90
b = 41.09	β = 96.35
c = 93.477	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-29 
Deposition Author(s): Liu, G.Z., Liu, W.D., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2017-03-29
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description