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- PDB-7w5h: The structure of trichobrasilenol synthase TaTC6 in complex with FsPP -

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Basic information

Entry
Database: PDB / ID: 7w5h
TitleThe structure of trichobrasilenol synthase TaTC6 in complex with FsPP
ComponentsTerpene cyclase 6
KeywordsLYASE/METAL BINDING PROTEIN / trichobrasilenol synthase / Trichoderma / sesquiterpene cyclase / farnesyl diphosphate / LYASE / LYASE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


(E)-2-epi-beta-caryophyllene synthase / (+)-isoafricanol synthase / pristinol synthase / (-)-beta-caryophyllene synthase / (-)-E-beta-caryophyllene synthase activity / alpha-humulene synthase / alpha-humulene synthase activity / Lyases; Carbon-oxygen lyases; Acting on phosphates / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Chem-FPS / MALONATE ION / Terpene cyclase 6
Similarity search - Component
Biological speciesTrichoderma atroviride (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChen, C. / Wang, T. / Yang, Y. / Zhang, L. / Ko, T. / Huang, J. / Guo, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: Structural insights into the cyclization of unusual brasilane-type sesquiterpenes.
Authors: Wang, T. / Yang, Y. / He, M. / Liu, M. / Huang, J.W. / Min, J. / Chen, C.C. / Liu, Y. / Zhang, L. / Guo, R.T.
History
DepositionNov 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Terpene cyclase 6
B: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5229
Polymers91,3802
Non-polymers1,1427
Water10,971609
1
A: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3075
Polymers45,6901
Non-polymers6174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area15550 Å2
MethodPISA
2
B: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2154
Polymers45,6901
Non-polymers5253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.559, 98.567, 72.355
Angle α, β, γ (deg.)90.000, 94.590, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Terpene cyclase 6 / Sesquiterpene synthase 6


Mass: 45690.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma atroviride (fungus) / Gene: tatc6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A5S9I252, Lyases; Carbon-oxygen lyases; Acting on phosphates, alpha-humulene synthase, (E)-2-epi-beta-caryophyllene synthase, (+)-isoafricanol synthase, pristinol synthase, (-)- ...References: UniProt: A0A5S9I252, Lyases; Carbon-oxygen lyases; Acting on phosphates, alpha-humulene synthase, (E)-2-epi-beta-caryophyllene synthase, (+)-isoafricanol synthase, pristinol synthase, (-)-beta-caryophyllene synthase

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Non-polymers , 5 types, 616 molecules

#2: 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.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 297 K / Method: evaporation / Details: 1.2 M Sodium malonate, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34318 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34318 Å / Relative weight: 1
ReflectionResolution: 2.05→33.9 Å / Num. obs: 91204 / % possible obs: 99.6 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.127 / Net I/σ(I): 7.1
Reflection shellResolution: 2.05→2.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2000 / CC1/2: 0.84 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
SAINTdata scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4okm

4okm


Resolution: 2.05→31.23 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 3841 4.21 %
Rwork0.2021 87363 -
obs0.204 91204 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.09 Å2 / Biso mean: 20.94 Å2 / Biso min: 5.18 Å2
Refinement stepCycle: final / Resolution: 2.05→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 70 614 6302
Biso mean--26.02 26.69 -
Num. residues----683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.33911280.25733058318691
2.08-2.10.26431510.24723046319791
2.1-2.130.29591280.22753070319891
2.13-2.160.26511170.23083022313991
2.16-2.190.26131420.22843219336194
2.19-2.230.2741470.23453088323595
2.23-2.270.30771330.2313234336795
2.27-2.30.24861460.22623181332796
2.3-2.350.29651500.21613215336596
2.35-2.390.27051340.22293226336097
2.39-2.440.29531410.22423201334297
2.44-2.490.30531710.22013268343997
2.49-2.550.24331100.21473262337298
2.55-2.620.27871670.21713296346399
2.62-2.690.22251420.20813330347299
2.69-2.760.25851550.215833123467100
2.76-2.850.25781400.21133323346399
2.85-2.960.25241400.2153323346399
2.96-3.070.25841620.20143313347599
3.07-3.210.2391310.20083369350099
3.21-3.380.19851500.18493265341599
3.38-3.60.25991410.18463333347499
3.6-3.870.21351440.17273271341598
3.87-4.260.17551480.16733275342398
4.26-4.870.21611410.17363297343898
4.88-6.130.24771400.19393299343999
6.14-31.230.22371420.18583267340998

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