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- PDB-8a7l: PcIDS1 in complex with Mg2+, GPP, and ZOL -

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Basic information

Entry
Database: PDB / ID: 8a7l
TitlePcIDS1 in complex with Mg2+, GPP, and ZOL
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 / ZOLEDRONIC ACID / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesPhaedon cochleariae (mustard beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 21, 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

Downloads & links

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Assembly

Deposited unit
A: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7307
Polymers39,9791
Non-polymers7516
Water3,189177
1
A: Isoprenyl diphosphate synthase
hetero molecules

A: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,46114
Polymers79,9582
Non-polymers1,50312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area8220 Å2
ΔGint-97 kcal/mol
Surface area27030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.170, 86.170, 119.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Isoprenyl diphosphate synthase


Mass: 39978.965 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 183 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID


Mass: 272.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O7P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS, 45% PEG 400

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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: Sep 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 43158 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.95 Å / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2 / Num. unique obs: 6361 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8A6U

8a6u


Resolution: 1.85→15 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 6.054 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 2153 5 %RANDOM
Rwork0.1474 ---
obs0.1492 40913 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.39 Å2 / Biso mean: 36.179 Å2 / Biso min: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å2-0 Å2
2---0.66 Å20 Å2
3---2.15 Å2
Refinement stepCycle: final / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2808 0 44 177 3029
Biso mean--33.92 43.49 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132933
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172730
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6533968
X-RAY DIFFRACTIONr_angle_other_deg1.2461.5746345
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.165351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88721.975157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6261519
X-RAY DIFFRACTIONr_chiral_restr0.0620.2374
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02624
X-RAY DIFFRACTIONr_rigid_bond_restr0.88235655
LS refinement shellResolution: 1.85→1.897 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 158 -
Rwork0.266 3008 -
all-3166 -
obs--99.03 %
Refinement TLS params.Method: refined / Origin x: -32.6212 Å / Origin y: 36.4606 Å / Origin z: 26.759 Å
111213212223313233
T0.0117 Å2-0.0212 Å2-0.0038 Å2-0.1131 Å2-0.0109 Å2--0.014 Å2
L1.0905 °2-0.337 °20.4051 °2-1.0566 °2-0.8336 °2--2.2228 °2
S0.0251 Å °0.1434 Å °0.0072 Å °-0.0062 Å °-0.0952 Å °0.066 Å °-0.0321 Å °-0.052 Å °0.0701 Å °

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