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- PDB-7bzc: Crystal structure of plant sesterterpene synthase AtTPS18 complex... -

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Basic information

Entry
Database: PDB / ID: 7bzc
TitleCrystal structure of plant sesterterpene synthase AtTPS18 complexed with farnesyl thiolodiphosphate (FSPP)
ComponentsTerpenoid synthase 18
KeywordsLYASE / terpenoid / terpene synthase / sesterterpene / cyclization mechanism / PLANT PROTEIN
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Terpene cyclase-like 1, C-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / : / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-FPS / Terpenoid synthase 18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsLi, J.X. / Wang, G.D. / Zhang, P.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFA0900600 China
National Natural Science Foundation of China (NSFC)31970315 China
National Natural Science Foundation of China (NSFC)31700263 China
Chinese Academy of SciencesZDRW-ZS-2019-2 China
Chinese Academy of SciencesXDB27020103 China
CitationJournal: Plant Commun. / Year: 2020
Title: Molecular Basis for Sesterterpene Diversity Produced by Plant Terpene Synthases.
Authors: Chen, Q. / Li, J. / Liu, Z. / Mitsuhashi, T. / Zhang, Y. / Liu, H. / Ma, Y. / He, J. / Shinada, T. / Sato, T. / Wang, Y. / Liu, H. / Abe, I. / Zhang, P. / Wang, G.
History
DepositionApr 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terpenoid synthase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9474
Polymers69,5001
Non-polymers4473
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-25 kcal/mol
Surface area22170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.388, 81.537, 125.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Terpenoid synthase 18 / Sesterterpene Synthase AtTPS18 / AtTPS18


Mass: 69500.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TPS18, At3g14520, MIE1.2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9LUE2, Lyases; Carbon-oxygen lyases; Acting on phosphates
#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: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16% (w/v) PEG 8000, 0.04M potassium phosphate (monobasic), 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.3→34.445 Å / Num. obs: 38230 / % possible obs: 99.7 % / Redundancy: 10.8 % / CC1/2: 0.998 / Net I/σ(I): 20
Reflection shellResolution: 2.303→2.385 Å / Num. unique obs: 2080 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EAT

5eat


Resolution: 2.303→34.445 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1911 5 %
Rwork0.2022 36319 -
obs0.2043 38230 67.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.95 Å2 / Biso mean: 38.2717 Å2 / Biso min: 14.87 Å2
Refinement stepCycle: final / Resolution: 2.303→34.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 57 87 4472
Biso mean--70.26 33.7 -
Num. residues----535
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.303-2.36030.3946690.3098131535
2.3603-2.42410.3406870.2942165843
2.4241-2.49540.3652940.2858178547
2.4954-2.57590.33821020.2778195351
2.5759-2.66790.3181070.2724202553
2.6679-2.77470.32871120.2696209955
2.7747-2.90090.32171190.2745222358
2.9009-3.05380.30441220.2709238162
3.0538-3.2450.29111410.2357269270
3.245-3.49530.26941670.2064316883
3.4953-3.84660.23911890.1944358493
3.8466-4.40230.22831940.1624378899
4.4023-5.54270.18042050.15823827100
5.5427-34.4450.17812030.1619382199

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