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- PDB-5hxn: Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M and ... -

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Basic information

Entry
Database: PDB / ID: 5hxn
TitleCrystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M and E75A mutants) from the Wild Tomato Solanum habrochaites
Components(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
KeywordsTRANSFERASE / prenyltransferase
Function / homology
Function and homology information


(2Z,6Z)-farnesyl diphosphate synthase / (2Z,6Z)-farnesyl diphosphate synthase activity / plastid membrane organization / ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity / polyprenol biosynthetic process / chloroplast stroma / response to cold / magnesium ion binding
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesSolanum habrochaites (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 aZ,Z-Farnesyl Diphosphate Synthase.
Authors: Chan, Y.T. / Ko, T.P. / Yao, S.H. / Chen, Y.W. / Lee, C.C. / Wang, A.H.
History
DepositionJan 31, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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


Theoretical massNumber of molelcules
Total (without water)26,7591
Polymers26,7591
Non-polymers00
Water2,756153
1
A: (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic

A: (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic


Theoretical massNumber of molelcules
Total (without water)53,5172
Polymers53,5172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3470 Å2
ΔGint-23 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.891, 51.891, 173.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

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


Mass: 26758.727 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-303
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.18 Å3/Da / Density % sol: 43.57 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 8
Details: 70% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Tris, pH 8.0.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 15386 / % possible obs: 97.4 % / Redundancy: 11 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 52.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 10 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 4.3 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JP3

1jp3


Resolution: 2.05→23.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.696 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24135 751 5 %RANDOM
Rwork0.19163 ---
obs0.19413 14337 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2---0.06 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.05→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 0 154 1925
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0191806
X-RAY DIFFRACTIONr_bond_other_d0.0010.021749
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9632432
X-RAY DIFFRACTIONr_angle_other_deg0.73534034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6595219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7242586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89415340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.301158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
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_it1.3492.626879
X-RAY DIFFRACTIONr_mcbond_other1.352.621878
X-RAY DIFFRACTIONr_mcangle_it2.253.9241097
X-RAY DIFFRACTIONr_mcangle_other2.2493.9311098
X-RAY DIFFRACTIONr_scbond_it1.6962.893927
X-RAY DIFFRACTIONr_scbond_other1.6962.898928
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8354.2371336
X-RAY DIFFRACTIONr_long_range_B_refined5.26121.332120
X-RAY DIFFRACTIONr_long_range_B_other4.921.0522078
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 43 -
Rwork0.216 850 -
obs--78.75 %

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