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- PDB-8h6u: Class I sesquiterpene synthase BCBOT2 (complex) -

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Basic information

Entry
Database: PDB / ID: 8h6u
TitleClass I sesquiterpene synthase BCBOT2 (complex)
ComponentsPresilphiperfolan-8-beta-ol synthase
KeywordsSTRUCTURAL PROTEIN / class I sesquiterpene synthase BCBOT2 (complex)
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
N-benzyl-N,N-diethylethanaminium / PYROPHOSPHATE 2- / Presilphiperfolan-8-beta-ol synthase
Similarity search - Component
Biological speciesBotrytis cinerea (gray fruit mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,99424
Polymers167,2304
Non-polymers1,76520
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-150 kcal/mol
Surface area50150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.544, 112.544, 253.567
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BTM / N-benzyl-N,N-diethylethanaminium


Mass: 192.320 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H22N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 18% w/v PEG 3350, 200 mM sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.78→63.39 Å / Num. obs: 47729 / % possible obs: 100 % / Redundancy: 19.9 % / Rmerge(I) obs: 0.193 / Net I/σ(I): 11.5
Reflection shellResolution: 2.78→2.88 Å / Rmerge(I) obs: 0.485 / Num. unique obs: 4609

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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: 8H6Q

8h6q


Resolution: 2.78→56.27 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2708 1978 4.19 %
Rwork0.2147 --
obs0.217 47243 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.78→56.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10869 0 104 425 11398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911241
X-RAY DIFFRACTIONf_angle_d0.9815270
X-RAY DIFFRACTIONf_dihedral_angle_d5.9951514
X-RAY DIFFRACTIONf_chiral_restr0.051594
X-RAY DIFFRACTIONf_plane_restr0.0081998
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.850.41691360.3073155X-RAY DIFFRACTION99
2.85-2.930.35741340.28583160X-RAY DIFFRACTION99
2.93-3.010.33731390.27463195X-RAY DIFFRACTION99
3.01-3.110.3131410.25873208X-RAY DIFFRACTION99
3.11-3.220.31321380.26413189X-RAY DIFFRACTION99
3.22-3.350.31111380.25493193X-RAY DIFFRACTION99
3.35-3.50.28011420.26283214X-RAY DIFFRACTION99
3.5-3.690.2731440.21673238X-RAY DIFFRACTION100
3.69-3.920.2911440.20863209X-RAY DIFFRACTION99
3.92-4.220.24871360.19143239X-RAY DIFFRACTION99
4.22-4.640.22711460.18323281X-RAY DIFFRACTION100
4.65-5.320.23351470.17463283X-RAY DIFFRACTION100
5.32-6.70.2271480.18633312X-RAY DIFFRACTION100
6.7-56.270.20281450.15053389X-RAY DIFFRACTION97

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