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- PDB-8a7u: PcIDS1_F315D in complex with Mg2+ and GPP -

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Basic information

Entry
Database: PDB / ID: 8a7u
TitlePcIDS1_F315D 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: 1.55 Å
AuthorsEcker, F. / Boland, F. / 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
B: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,4229
Polymers79,8942
Non-polymers5287
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-69 kcal/mol
Surface area28390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.970, 78.120, 88.130
Angle α, β, γ (deg.)90.000, 101.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Isoprenyl diphosphate synthase


Mass: 39946.879 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.: 5 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 0.5 M LiCl, 28% PEG 6000

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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: 1.55→30 Å / Num. obs: 107827 / % possible obs: 94.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.1
Reflection shellResolution: 1.55→1.65 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 18942 / % possible all: 98.2

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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: 1.55→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 3.25 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1865 5392 5 %RANDOM
Rwork0.146 ---
obs0.1481 102435 94.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.64 Å2 / Biso mean: 26.745 Å2 / Biso min: 15.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.59 Å2
2---0.45 Å20 Å2
3----0.81 Å2
Refinement stepCycle: final / Resolution: 1.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 30 398 5742
Biso mean--25.35 34.5 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175149
X-RAY DIFFRACTIONr_angle_refined_deg1.7851.6477399
X-RAY DIFFRACTIONr_angle_other_deg1.561.57511975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38622.226292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.785151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.81534
X-RAY DIFFRACTIONr_chiral_restr0.1040.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021151
X-RAY DIFFRACTIONr_rigid_bond_restr3.46310628
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 413 -
Rwork0.263 7840 -
all-8253 -
obs--98.57 %
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)
10.89070.64440.21631.38010.3730.8273-0.0058-0.13030.05380.10810.00280.0674-0.06020.00180.00290.04050.0209-0.00770.0444-0.00250.024770.21889.510332.3895
20.8178-0.7089-0.11991.3196-0.01750.2792-0.02780.076-0.0178-0.03840.0273-0.03310.01190.08210.00040.0109-0.0125-0.00630.0692-0.01160.031975.209-11.06515.9508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A86 - 427
2X-RAY DIFFRACTION2B86 - 426

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