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- PDB-8a73: PcIDS1 in complex with Mn2+ and GPP -

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Basic information

Entry
Database: PDB / ID: 8a73
TitlePcIDS1 in complex with Mn2+ and GPP
ComponentsIsoprenyl diphosphate synthase
KeywordsBIOSYNTHETIC PROTEIN / Insects / Biosynthesis / Terpenes / Metal regulation / Catalysis
Function / homology
Function and homology information


pheromone biosynthetic process / dimethylallyltranstransferase activity / isoprenoid biosynthetic process / metal ion binding
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: 1.6 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)81,0599
Polymers79,9582
Non-polymers1,1017
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-51 kcal/mol
Surface area29350 Å2
Unit cell
Length a, b, c (Å)59.060, 78.410, 87.300
Angle α, β, γ (deg.)90.000, 101.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoprenyl diphosphate synthase


Mass: 39978.965 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE / Geranyl pyrophosphate


Mass: 314.209 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.4 M K-Formate, 19% 3350

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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: Apr 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 97381 / % possible obs: 94.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 10.1
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 2 / Num. unique obs: 16625 / % possible all: 97.8

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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: 1.6→15 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.175 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 4863 5 %RANDOM
Rwork0.1596 ---
obs0.1613 92404 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.41 Å2 / Biso mean: 29.602 Å2 / Biso min: 16.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å20.03 Å2
2---2.62 Å20 Å2
3---1.79 Å2
Refinement stepCycle: final / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5455 0 80 346 5881
Biso mean--37.87 38.89 -
Num. residues----671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135748
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175380
X-RAY DIFFRACTIONr_angle_refined_deg1.1861.6537779
X-RAY DIFFRACTIONr_angle_other_deg1.2411.57412504
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2155691
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52921.815314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.507151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3481537
X-RAY DIFFRACTIONr_chiral_restr0.0640.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026342
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021229
X-RAY DIFFRACTIONr_rigid_bond_restr0.656311128
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 368 -
Rwork0.265 7008 -
all-7376 -
obs--98.25 %
Refinement TLS params.

S32: 0.0003 Å ° / T13: -0.0018 Å2 / 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 °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.01120.01960.00730.03960.01680.0178-0.0016-0.00210.00140.00010.00090.0016-0.00070.00080.0040.00030.02170.00010.000911.29839.939232.18
20.0128-0.0082-0.00290.01990.00780.0052-0.0018-0.0008-0.00050.00020.00150.001-0.00040.00030.0041-0.00010.02110.00020.00116.4886-10.95375.8752
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 429
2X-RAY DIFFRACTION2B86 - 427

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