5HXT

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with IPP and DMSPP

• PDB DOI: https://doi.org/10.2210/pdb5HXT/pdb

• Classification: TRANSFERASE
• Organism(s): Solanum habrochaites
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-01-31 Released: 2017-04-05 
• Deposition Author(s): Lee, C.C., Chan, Y.T., Wang, A.H.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.249 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure and Potential Head-to-Middle Condensation Function of a Z,Z-Farnesyl Diphosphate Synthase

Chan, Y.T., Ko, T.P., Yao, S.H., Chen, Y.W., Lee, C.C., Wang, A.H.J.

(2017) ACS Omega 2: 930-936

• DOI: https://doi.org/10.1021/acsomega.6b00562

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)

Macromolecule Content

• Total Structure Weight: 54.9 kDa 
• Atom Count: 4,002 
• Modelled Residue Count: 447 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic	A, B	233	Solanum habrochaites	Mutation(s): 2  Gene Names: ZFPS EC: 2.5.1.92
UniProt
Find proteins for B8XA40 (Solanum habrochaites) Explore B8XA40  Go to UniProtKB:  B8XA40

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O4B	I [auth B]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C12 H24 O6 XEZNGIUYQVAUSS-UHFFFAOYSA-N
DST	D [auth A], G [auth B]	DIMETHYLALLYL S-THIOLODIPHOSPHATE C5 H12 O6 P2 S ZWFWSISPSBLNGO-UHFFFAOYSA-N
IPR	E [auth A], H [auth B]	ISOPENTYL PYROPHOSPHATE C5 H14 O7 P2 IPFXNYPSBSIFOB-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.249 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.981	α = 90
b = 66.321	β = 90
c = 128.939	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): Lee, C.C., Chan, Y.T., Wang, A.H.J.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 2.0: 2019-10-16
  Changes: Data collection, Database references, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary