[English] 日本語
Yorodumi
- PDB-6b06: Crystal structure of CfFPPS2, a lepidopteran type-II farnesyl dip... -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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
Revision 2.0May 1, 2024Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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-(2,2-diphosphonoethyl)-1-methylpyridin-1-ium


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


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


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more