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- PDB-8a74: PcIDS1_F315A in complex with Mg2+ and GPP -

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Basic information

Entry
Database: PDB / ID: 8a74
TitlePcIDS1_F315A in complex with Mg2+ and GPP
ComponentsIsoprenyl diphosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / Insects / Biosynthesis / Terpenes / Metal regulation / Catalysis
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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
GERANYL DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesPhaedon cochleariae (mustard beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEcker, F. / Boland, W. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GR_1861/5-2 Germany
CitationJournal: Nat.Chem. / Year: 2023
Title: Metal-dependent enzyme symmetry guides the biosynthetic flux of terpene precursors.
Authors: Ecker, F. / Vattekkatte, A. / Boland, W. / Groll, M.
History
DepositionJun 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 16, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoprenyl diphosphate synthase
B: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,62912
Polymers79,8062
Non-polymers82310
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.210, 78.250, 89.260
Angle α, β, γ (deg.)90.000, 101.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoprenyl diphosphate synthase


Mass: 39902.867 Da / Num. of mol.: 2 / Mutation: F315A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaedon cochleariae (mustard beetle) / Production host: Escherichia coli (E. coli) / References: UniProt: M1JS91, dimethylallyltranstransferase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, 0.2 M MgCl2, 25% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 61843 / % possible obs: 98.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 8868 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A6U

8a6u


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.38 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 3086 5 %RANDOM
Rwork0.1997 ---
obs0.2017 58621 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.7 Å2 / Biso mean: 34.126 Å2 / Biso min: 20.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.89 Å20 Å22.28 Å2
2--0.25 Å2-0 Å2
3---1.55 Å2
Refinement stepCycle: final / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5309 0 46 222 5577
Biso mean--37.79 39.57 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135489
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175160
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.6497415
X-RAY DIFFRACTIONr_angle_other_deg1.1581.57511996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1545656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32422.075294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.663151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7591535
X-RAY DIFFRACTIONr_chiral_restr0.0560.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021146
X-RAY DIFFRACTIONr_rigid_bond_restr0.472310649
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 225 -
Rwork0.3 4275 -
all-4500 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.02491.07970.2891.97750.60330.9013-0.017-0.21490.00410.07480.02230.0324-0.06850.065-0.00530.15680.0262-0.03020.12010.00650.010911.23269.700332.8179
21.3006-0.9937-0.08571.5534-0.0060.4196-0.03630.084-0.0204-0.04710.0349-0.03730.01410.12960.00140.1144-0.0196-0.02970.0862-0.0060.015616.4873-10.65786.0093
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A87 - 427
2X-RAY DIFFRACTION2B87 - 427

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