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- PDB-8a6u: PcIDS1 in complex with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 8a6u
TitlePcIDS1 in complex with Mg2+
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
Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesPhaedon cochleariae (mustard beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)80,0074
Polymers79,9582
Non-polymers492
Water10,701594
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)59.160, 78.330, 89.610
Angle α, β, γ (deg.)90.000, 101.710, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 51.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 0.2 M MgCl2, 20% PEG 8000

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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: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 94381 / % possible obs: 98 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 16.4
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 15316

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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: 1UBX

1ubx


Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.965 / SU B: 6.381 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 4712 5 %RANDOM
Rwork0.1553 ---
obs0.1573 89539 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.16 Å2 / Biso mean: 36.621 Å2 / Biso min: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1-4.33 Å20 Å23.05 Å2
2---4.71 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 2 594 5786
Biso mean--37.59 54.4 -
Num. residues----640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135306
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175001
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.6447161
X-RAY DIFFRACTIONr_angle_other_deg1.2611.57411630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1395635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.14622.657271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37315978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4421528
X-RAY DIFFRACTIONr_chiral_restr0.0650.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021100
X-RAY DIFFRACTIONr_rigid_bond_restr7.58310307
LS refinement shellResolution: 1.65→1.692 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 348 -
Rwork0.276 6620 -
all-6968 -
obs--98.63 %

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