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- PDB-6b06: Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl dip... -

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Basic information

Entry
Database: PDB / ID: 6b06
TitleCrystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with IPP and [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid (inhibitor 1b)
ComponentsFarnesyl diphosphate synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / juvenile hormone / farnesyl diphosphate synthase / inhibitor design / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


pheromone biosynthetic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / isoprenoid biosynthetic process
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
Chem-C6J / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
C: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,28718
Polymers117,4833
Non-polymers1,80315
Water99155
1
A: Farnesyl diphosphate synthase
B: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,52412
Polymers78,3222
Non-polymers1,20210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-94 kcal/mol
Surface area27050 Å2
MethodPISA
2
C: Farnesyl diphosphate synthase
hetero molecules

C: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,52412
Polymers78,3222
Non-polymers1,20210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5640 Å2
ΔGint-95 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.219, 122.646, 68.145
Angle α, β, γ (deg.)90.000, 107.050, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 39161.051 Da / Num. of mol.: 3 / 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
#2: Chemical ChemComp-C6J / [2-(1-methylpyridin-2-yl)-1-phosphono-ethyl]phosphonic acid


Mass: 282.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H14NO6P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.18 Å3/Da / Density % sol: 61.36 % / Mosaicity: 0.45 °
Crystal growTemperature: 295 K / Method: microbatch / Details: 20% PEG3350, 0.2 M ammonium formate

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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: 2.6→101.17 Å / Num. obs: 44753 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.066 / Rrim(I) all: 0.126 / Χ2: 2.098 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6930.76544440.5970.5170.9271.1699.6
2.69-2.83.60.75644630.6920.4670.891.228100
2.8-2.933.80.61544690.8260.3660.7161.308100
2.93-3.083.80.49344630.8480.2920.5741.397100
3.08-3.283.80.32444940.9290.1930.3771.615100
3.28-3.533.80.20444250.9630.1220.2381.87899.9
3.53-3.883.70.1345000.9820.0790.1522.19199.9
3.88-4.453.70.08744660.990.0530.1022.79699.7
4.45-5.63.70.07345040.9910.0450.0863.37499.8
5.6-503.40.05445250.9970.0350.0653.99899.3

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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: 2.6→101.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 11.443 / SU ML: 0.23 / SU R Cruickshank DPI: 0.4594 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.459 / ESU R Free: 0.275
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 2258 5 %RANDOM
Rwork0.1841 ---
obs0.1867 42494 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.15 Å2 / Biso mean: 70.508 Å2 / Biso min: 33.79 Å2
Baniso -1Baniso -2Baniso -3
1--2.67 Å20 Å2-0.37 Å2
2--1.94 Å20 Å2
3---0.8 Å2
Refinement stepCycle: final / Resolution: 2.6→101.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8115 0 102 55 8272
Biso mean--70.59 58.14 -
Num. residues----1010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198383
X-RAY DIFFRACTIONr_bond_other_d0.0040.027977
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.98311363
X-RAY DIFFRACTIONr_angle_other_deg1.0813.00118413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38951006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60224.891368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.638151512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7271528
X-RAY DIFFRACTIONr_chiral_restr0.0940.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021846
LS refinement shellResolution: 2.605→2.673 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 162 -
Rwork0.294 2937 -
all-3099 -
obs--93.88 %

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