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- PDB-6b02: Crystal structure of CfFPPS2 (apo form), a lepidopteran type-II f... -

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Basic information

Entry
Database: PDB / ID: 6b02
TitleCrystal structure of CfFPPS2 (apo form), a lepidopteran type-II farnesyl diphosphate synthase
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE / juvenile hormone / farnesyl diphosphate synthase
Function / homology
Function and homology information


pheromone biosynthetic process / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 Å
AuthorsPicard, M.-E. / Cusson, M. / Shi, R.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)436202 Canada
CitationJournal: Insect Biochem. Mol. Biol. / Year: 2017
Title: Structural characterization of a lepidopteran type-II farnesyl diphosphate synthase from the spruce budworm, Choristoneura fumiferana: Implications for inhibitor design.
Authors: Picard, M.E. / Nisole, A. / Beliveau, C. / Sen, S. / Barbar, A. / Shi, R. / Cusson, M.
History
DepositionSep 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: Farnesyl diphosphate synthase
B: Farnesyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)78,3222
Polymers78,3222
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.679, 113.679, 131.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Farnesyl diphosphate synthase / CfFPPS2 / type-II farnesyl diphosphate synthase


Mass: 39161.051 Da / Num. of mol.: 2 / Fragment: UNP residues 57-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Choristoneura fumiferana (eastern spruce budworm)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 (DE3)
References: UniProt: Q1XAB1, Transferases; Transferring alkyl or aryl groups, other than methyl groups

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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: 3.13 Å3/Da / Density % sol: 60.72 % / Mosaicity: 0.997 °
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.6 / Details: 20% PEG4000, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 20, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.82→98.45 Å / Num. obs: 23898 / % possible obs: 99.5 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Χ2: 1.138 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.82-2.929.80.99922420.8360.3270.96795.2
2.92-3.0410.90.80223710.9140.2540.99799.90.842
3.04-3.1811.10.54923580.9610.1721.0761000.575
3.18-3.3411.20.3523880.9840.1091.21000.366
3.34-3.5511.20.21423790.9930.0671.3831000.224
3.55-3.83100.17923580.9920.0591.62399.90.188
3.83-4.2111.10.09824100.9980.031.0321000.102
4.21-4.8211.10.07424160.9980.0231.1021000.078
4.82-6.07110.06324230.9990.021.0171000.066
6.07-5010.50.03125530.9990.011.00699.80.033

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YV5

1yv5


Resolution: 2.82→98.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.911 / SU B: 26.119 / SU ML: 0.443 / SU R Cruickshank DPI: 1.3114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.311 / ESU R Free: 0.415
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2958 1214 5.1 %RANDOM
Rwork0.2161 ---
obs0.2198 22500 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 212.44 Å2 / Biso mean: 105.202 Å2 / Biso min: 59.92 Å2
Baniso -1Baniso -2Baniso -3
1--5.8 Å2-2.9 Å20 Å2
2---5.8 Å2-0 Å2
3---18.81 Å2
Refinement stepCycle: final / Resolution: 2.82→98.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5324 0 0 0 5324
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195436
X-RAY DIFFRACTIONr_bond_other_d0.0020.025177
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.977365
X-RAY DIFFRACTIONr_angle_other_deg1.021311941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.625661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36724.728239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.43515977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3711520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026025
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021199
LS refinement shellResolution: 2.824→2.897 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 94 -
Rwork0.381 1541 -
all-1635 -
obs--93 %

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