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- PDB-5hxq: Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75... -

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Basic information

Entry
Database: PDB / ID: 5hxq
TitleCrystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with DMSPP
Components(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


(2Z,6Z)-farnesyl diphosphate synthase / 2-cis,6-cis-farnesyl pyrophosphate synthase activity / prenyltransferase activity / chloroplast / magnesium ion binding
Similarity search - Function
Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIMETHYLALLYL S-THIOLODIPHOSPHATE / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesSolanum habrochaites (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLee, C.C. / Chan, Y.T. / Wang, A.H.J.
CitationJournal: Acs Omega / Year: 2017
Title: Crystal Structure and Potential Head-to-Middle Condensation Function of a Z,Z-Farnesyl Diphosphate Synthase
Authors: Chan, Y.T. / Ko, T.P. / Yao, S.H. / Chen, Y.W. / Lee, C.C. / Wang, A.H.J.
History
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 16, 2019Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / citation / entity
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _citation.country / _citation.journal_id_ISSN / _entity.formula_weight
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
C: (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3585
Polymers53,5682
Non-polymers7913
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-25 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.752, 66.800, 128.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic / Z / Z-FPP synthase / Z-farnesyl pyrophosphate synthase


Mass: 26783.754 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 72-303 / Mutation: E75A, H103Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum habrochaites (plant) / Gene: ZFPS / Plasmid: pET-32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: B8XA40, (2Z,6Z)-farnesyl diphosphate synthase
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / 18-Crown-6


Mass: 264.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: 13% PEG 10K, 20mM 18-crown-6, 0.1M MES, pH 6.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 38064 / % possible obs: 99.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 42.4
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.76 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data processing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HXN

5hxn


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.168 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24128 1679 5 %RANDOM
Rwork0.19397 ---
obs0.1964 31779 87.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.882 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0 Å2
2--1.26 Å2-0 Å2
3----0.79 Å2
Refinement stepCycle: 1 / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 50 347 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023763
X-RAY DIFFRACTIONr_bond_other_d0.0030.023652
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9775053
X-RAY DIFFRACTIONr_angle_other_deg1.1293.0118425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5295448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17424.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8715703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6381520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02856
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4792.831798
X-RAY DIFFRACTIONr_mcbond_other1.4772.8281797
X-RAY DIFFRACTIONr_mcangle_it2.4664.2342244
X-RAY DIFFRACTIONr_mcangle_other2.4674.2362245
X-RAY DIFFRACTIONr_scbond_it1.8443.1891965
X-RAY DIFFRACTIONr_scbond_other1.8443.191966
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0854.6352810
X-RAY DIFFRACTIONr_long_range_B_refined5.84423.4224508
X-RAY DIFFRACTIONr_long_range_B_other5.56123.0054383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 65 -
Rwork0.232 1273 -
obs--48.46 %

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