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- PDB-6b07: Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl dip... -

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Basic information

Entry
Database: PDB / ID: 6b07
TitleCrystal structure of CfFPPS2, a lepidopteran type-II farnesyl diphosphate synthase, complexed with [1-phosphono-2-(1-propylpyridin-2-yl)ethyl]phosphonic acid (inhibitor 1d)
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-C6M / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesChoristoneura fumiferana (eastern spruce budworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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)119,06722
Polymers117,4833
Non-polymers1,58419
Water16,412911
1
A: Farnesyl diphosphate synthase
B: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,33714
Polymers78,3222
Non-polymers1,01512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-83 kcal/mol
Surface area26960 Å2
MethodPISA
2
C: Farnesyl diphosphate synthase
hetero molecules

C: Farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46116
Polymers78,3222
Non-polymers1,13914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6010 Å2
ΔGint-60 kcal/mol
Surface area26460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.913, 122.579, 69.064
Angle α, β, γ (deg.)90.000, 106.510, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-723-

HOH

21C-797-

HOH

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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-C6M / [1-phosphono-2-(1-propylpyridin-2-yl)ethyl]phosphonic acid


Mass: 310.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18NO6P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 3.23 Å3/Da / Density % sol: 61.9 % / Mosaicity: 0.58 °
Crystal growTemperature: 295 K / Method: microbatch / Details: 20% PEG3350, 0.2 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.98→101.18 Å / Num. obs: 99585 / % possible obs: 96 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Χ2: 1.007 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.053.10.53684510.7350.3510.6430.99882
2.05-2.133.80.41798740.850.2470.4851.00295.5
2.13-2.233.80.29999510.9270.1760.3481.01196.1
2.23-2.353.80.24499820.9540.1440.2841.03396.6
2.35-2.493.80.186100320.9720.1090.2161.01797.1
2.49-2.693.80.137101000.9840.0810.1591.01197.5
2.69-2.963.80.101101450.9910.0590.1171.0198.1
2.96-3.393.80.066102650.9960.0390.0770.99398.7
3.39-4.263.80.041103180.9970.0240.0470.99499.2
4.26-503.80.028104670.9990.0170.033199.5

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Processing

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

1yv5


Resolution: 1.98→101.18 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.474 / SU ML: 0.095 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 4966 5 %RANDOM
Rwork0.1709 ---
obs0.1728 94476 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.02 Å2 / Biso mean: 32.884 Å2 / Biso min: 12.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å2-0 Å2-0.13 Å2
2---0.42 Å20 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 1.98→101.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8148 0 94 911 9153
Biso mean--30.14 41.9 -
Num. residues----1013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198425
X-RAY DIFFRACTIONr_bond_other_d0.0030.028050
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.97911405
X-RAY DIFFRACTIONr_angle_other_deg1.153.00118587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56251018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43424.758372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.129151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.771531
X-RAY DIFFRACTIONr_chiral_restr0.1340.21289
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021864
LS refinement shellResolution: 1.979→2.03 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 295 -
Rwork0.255 5648 -
all-5943 -
obs--77.71 %

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