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- PDB-8h6q: Class I sesquiterpene synthase BCBOT2 (apo) -

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Basic information

Entry
Database: PDB / ID: 8h6q
TitleClass I sesquiterpene synthase BCBOT2 (apo)
ComponentsPresilphiperfolan-8-beta-ol synthase
KeywordsSTRUCTURAL PROTEIN / class I sesquiterpene synthase BCBOT2 (apo)
Function / homology
Function and homology information


presilphiperfolanol synthase / sesquiterpene synthase activity / sesquiterpene biosynthetic process / farnesyl diphosphate metabolic process / magnesium ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Presilphiperfolan-8-beta-ol synthase
Similarity search - Component
Biological speciesBotrytis cinerea (gray fruit mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLou, T.T. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22077007, 21877002 China
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Structural Insights into Three Sesquiterpene Synthases for the Biosynthesis of Tricyclic Sesquiterpenes and Chemical Space Expansion by Structure-Based Mutagenesis.
Authors: Lou, T. / Li, A. / Xu, H. / Pan, J. / Xing, B. / Wu, R. / Dickschat, J.S. / Yang, D. / Ma, M.
History
DepositionOct 18, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Presilphiperfolan-8-beta-ol synthase
B: Presilphiperfolan-8-beta-ol synthase
C: Presilphiperfolan-8-beta-ol synthase
D: Presilphiperfolan-8-beta-ol synthase


Theoretical massNumber of molelcules
Total (without water)167,2304
Polymers167,2304
Non-polymers00
Water27,4371523
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.613, 116.611, 88.115
Angle α, β, γ (deg.)90.00, 111.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Presilphiperfolan-8-beta-ol synthase / PSPS / Botrydial synthesis protein 2 / Calcineurin-dependent protein 15 / Sesquiterpene cyclase ...PSPS / Botrydial synthesis protein 2 / Calcineurin-dependent protein 15 / Sesquiterpene cyclase BOT2 / Sesquiterpene synthase BOT2


Mass: 41807.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Botrytis cinerea (gray fruit mold) / Gene: BOT2, CND15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6WP50, presilphiperfolanol synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1523 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M MgCl2, 0.1 M Sodium HEPES, 10% w/v PEG 4000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 126269 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.8
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.507 / Num. unique obs: 6294

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold 2 prediction

Resolution: 2→40.7 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 5326 5.01 %
Rwork0.1675 --
obs0.1689 106371 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10494 0 0 1523 12017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710999
X-RAY DIFFRACTIONf_angle_d0.74814927
X-RAY DIFFRACTIONf_dihedral_angle_d5.0751472
X-RAY DIFFRACTIONf_chiral_restr0.0451575
X-RAY DIFFRACTIONf_plane_restr0.0081959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.23611780.20773258X-RAY DIFFRACTION97
2.02-2.050.22852020.20733351X-RAY DIFFRACTION100
2.05-2.070.22131780.19573387X-RAY DIFFRACTION99
2.07-2.10.23841720.18723369X-RAY DIFFRACTION100
2.1-2.130.231990.18143334X-RAY DIFFRACTION99
2.13-2.150.20691860.17783323X-RAY DIFFRACTION98
2.15-2.190.22141920.17293310X-RAY DIFFRACTION98
2.19-2.220.21111790.17763280X-RAY DIFFRACTION96
2.22-2.250.21071860.17393276X-RAY DIFFRACTION97
2.25-2.290.20721690.16833368X-RAY DIFFRACTION99
2.29-2.330.18061700.17373425X-RAY DIFFRACTION100
2.33-2.370.20461630.17683370X-RAY DIFFRACTION100
2.37-2.420.22691480.17263411X-RAY DIFFRACTION100
2.42-2.470.21291540.16673387X-RAY DIFFRACTION100
2.47-2.520.18641910.16543388X-RAY DIFFRACTION100
2.52-2.580.15981770.16763394X-RAY DIFFRACTION100
2.58-2.640.20972020.16963348X-RAY DIFFRACTION100
2.64-2.710.19661650.16813409X-RAY DIFFRACTION99
2.71-2.790.21681840.16073349X-RAY DIFFRACTION99
2.79-2.880.18731860.16263362X-RAY DIFFRACTION99
2.88-2.990.19472060.17123369X-RAY DIFFRACTION100
2.99-3.110.2151610.1663441X-RAY DIFFRACTION100
3.11-3.250.2031900.16353415X-RAY DIFFRACTION100
3.25-3.420.18151720.16823367X-RAY DIFFRACTION100
3.42-3.630.19231650.15393409X-RAY DIFFRACTION100
3.63-3.910.1581580.1463427X-RAY DIFFRACTION100
3.91-4.310.14211570.14363217X-RAY DIFFRACTION94
4.31-4.930.16121930.14883410X-RAY DIFFRACTION100
4.93-6.210.21191530.18873453X-RAY DIFFRACTION100
6.21-40.70.22711900.1813438X-RAY DIFFRACTION99

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