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- PDB-7w5i: The structure of trichobrasilenol synthase TaTC6 in complex with FPP-1 -

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Basic information

Entry
Database: PDB / ID: 7w5i
TitleThe structure of trichobrasilenol synthase TaTC6 in complex with FPP-1
ComponentsTerpene cyclase 6
KeywordsLYASE/METAL BINDING PROTEIN / trichobrasilenol synthase / Trichoderma / sesquiterpene cyclase / farnesyl diphosphate / METAL BINDING PROTEIN / 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 / isoprenoid biosynthetic process / metal 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
FARNESYL DIPHOSPHATE / MALONATE ION / Terpene cyclase 6
Similarity search - Component
Biological speciesTrichoderma atroviride (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 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 1.0Jun 1, 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)93,09716
Polymers91,3802
Non-polymers1,71614
Water13,619756
1
A: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3936
Polymers45,6901
Non-polymers7035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-6 kcal/mol
Surface area15050 Å2
MethodPISA
2
B: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,70410
Polymers45,6901
Non-polymers1,0139
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-5 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.638, 98.336, 72.379
Angle α, β, γ (deg.)90.000, 94.650, 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, 770 molecules

#2: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE


Mass: 382.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 756 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 298 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: 1.34138 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.13→33.3 Å / Num. obs: 91204 / % possible obs: 98.3 % / Redundancy: 4 % / CC1/2: 1 / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.6
Reflection shellResolution: 2.13→2.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1664 / CC1/2: 0.92 / % possible all: 95.9

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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: 2.13→33.3 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 3751 4.77 %
Rwork0.2009 74934 -
obs0.2023 78685 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.49 Å2 / Biso mean: 20.6887 Å2 / Biso min: 3.89 Å2
Refinement stepCycle: final / Resolution: 2.13→33.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 110 759 6441
Biso mean--29.03 28.32 -
Num. residues----678
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 (%)
2.13-2.160.27691370.24062433257084
2.16-2.190.23571060.2332608271484
2.19-2.220.23071250.23042458258386
2.22-2.250.29551600.23942603276387
2.25-2.280.26481130.23072562267587
2.28-2.320.2321100.22422604271488
2.32-2.350.26711390.222671281089
2.35-2.390.25531130.22182701281490
2.39-2.440.28011560.22562639279591
2.44-2.490.28231310.22752779291092
2.49-2.540.22451500.20612710286093
2.54-2.590.2531190.2182862298195
2.59-2.650.26111340.21172783291796
2.65-2.720.26131580.21442911306997
2.72-2.790.241340.2082866300098
2.79-2.870.29021720.20112877304998
2.87-2.970.20591350.20622884301998
2.97-3.070.22021450.20352933307898
3.07-3.190.22341400.20332891303198
3.19-3.340.18961500.18742893304398
3.34-3.520.23751340.18452912304698
3.52-3.740.20671520.17352875302798
3.74-4.020.19361480.16372877302597
4.02-4.430.18381510.1662861301297
4.43-5.070.2071470.18432917306498
5.07-6.370.25911460.21532924307099
6.38-33.30.21741460.20562900304698

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