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- PDB-8a6z: PcIDS1 in complex with Mn2+ and IPP -

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Basic information

Entry
Database: PDB / ID: 8a6z
TitlePcIDS1 in complex with Mn2+ and IPP
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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / : / TRIETHYLENE GLYCOL / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesPhaedon cochleariae (mustard beetle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

Downloads & links

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Assembly

Deposited unit
A: Isoprenyl diphosphate synthase
B: Isoprenyl diphosphate synthase
C: Isoprenyl diphosphate synthase
D: Isoprenyl diphosphate synthase
E: Isoprenyl diphosphate synthase
F: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,15039
Polymers239,8746
Non-polymers4,27633
Water7,927440
1
A: Isoprenyl diphosphate synthase
C: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,42213
Polymers79,9582
Non-polymers1,46411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8640 Å2
ΔGint-68 kcal/mol
Surface area27250 Å2
MethodPISA
2
B: Isoprenyl diphosphate synthase
D: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,36413
Polymers79,9582
Non-polymers1,40611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-77 kcal/mol
Surface area26940 Å2
MethodPISA
3
E: Isoprenyl diphosphate synthase
F: Isoprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,36413
Polymers79,9582
Non-polymers1,40611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-75 kcal/mol
Surface area27090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.940, 186.740, 213.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Isoprenyl diphosphate synthase


Mass: 39978.965 Da / Num. of mol.: 6
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, 473 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H12O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS, 0.2 M MgCl2, 26% PEG 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: 2.4→30 Å / Num. obs: 90473 / % possible obs: 98.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 10.5
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 10308 / % possible all: 99

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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: 2.4→15 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.877 / SU B: 23.902 / SU ML: 0.247 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 4502 5 %RANDOM
Rwork0.2236 ---
obs0.2258 85538 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.44 Å2 / Biso mean: 33.777 Å2 / Biso min: 12.48 Å2
Baniso -1Baniso -2Baniso -3
1--5.95 Å20 Å2-0 Å2
2--7.31 Å20 Å2
3----1.37 Å2
Refinement stepCycle: final / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16705 0 208 446 17359
Biso mean--33.59 45.21 -
Num. residues----2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01317290
X-RAY DIFFRACTIONr_bond_other_d0.0020.01716103
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.65123359
X-RAY DIFFRACTIONr_angle_other_deg1.1191.57437412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4952049
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27822.208924
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.676153130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2815111
X-RAY DIFFRACTIONr_chiral_restr0.050.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0218943
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023670
X-RAY DIFFRACTIONr_rigid_bond_restr0.96333393
LS refinement shellResolution: 2.4→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 322 -
Rwork0.266 6111 -
all-6433 -
obs--98.97 %
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)
10.08290.00980.03170.0155-0.01760.04630.00130.00160-0.0021-0.00170.00140.00480.00070.00040.04930.0018-0.00010.0032-0.0040.03295.18117.816638.7905
20.06120.006-0.03890.01190.01620.0911-0.0016-0.0039-0.00350.00410.0003-0.00370.0044-0.00180.00130.04940.0019-0.00010.0012-0.00040.033424.7405-13.49852.7079
30.1703-0.007-0.05910.00170.00730.0780.00330.02690.01750.00110.00010.0002-0.00290.0027-0.00340.04820.0002-0.00160.00720.0070.033813.215132.400118.2314
40.0902-0.00490.02580.01390.00450.0489-0.00210.0023-0.00380.001-0.0024-0.00250.00050.00210.00460.04790.00050.00260.0028-0.00030.03316.9447-38.0617-17.9661
50.0223-0.0090.04750.0369-0.00710.10620.00060.0007-0.00120.000100.0022-0.00380.0015-0.00060.0460.00030.001200.00010.03634.29510.8734-30.4362
60.0592-0.0111-0.02580.0448-0.00780.0150.0030.0134-0.00340.005-0.0053-0.0025-0.0046-0.0050.00230.04990.0007-0.00180.00340.00210.03311.487738.491-47.0809
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A85 - 429
2X-RAY DIFFRACTION2B85 - 429
3X-RAY DIFFRACTION3C84 - 429
4X-RAY DIFFRACTION4D85 - 429
5X-RAY DIFFRACTION5E85 - 429
6X-RAY DIFFRACTION6F85 - 429

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