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- PDB-7w5f: The apo structure of trichobrasilenol synthase TaTC6 with the spa... -

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Basic information

Entry
Database: PDB / ID: 7w5f
TitleThe apo structure of trichobrasilenol synthase TaTC6 with the space group of monoclinic
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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Biological speciesTrichoderma atroviride (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 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)91,4294
Polymers91,3802
Non-polymers492
Water3,981221
1
A: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7152
Polymers45,6901
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area15040 Å2
MethodPISA
2
B: Terpene cyclase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7152
Polymers45,6901
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-9 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.984, 97.791, 72.296
Angle α, β, γ (deg.)90.000, 94.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
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: May 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.5→36.2 Å / Num. obs: 48370 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.156 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1102 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SAINTdata scaling
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4okm

4okm


Resolution: 2.53→36.19 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 3822 7.9 %
Rwork0.1879 44548 -
obs0.1931 48370 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.69 Å2 / Biso mean: 28.7367 Å2 / Biso min: 10.65 Å2
Refinement stepCycle: final / Resolution: 2.53→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 2 221 5789
Biso mean--37.69 28.77 -
Num. residues----677
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 (%)
2.53-2.560.30711200.22921706182698
2.56-2.60.29681600.23031636179698
2.6-2.630.31881340.23781583171799
2.63-2.670.32321350.23461711184699
2.67-2.710.27591290.2311692182199
2.71-2.750.27991500.23511583173398
2.75-2.80.28671470.22961688183598
2.8-2.840.31571490.22551654180399
2.84-2.90.3261540.22061659181398
2.9-2.950.26291240.21011640176499
2.95-3.010.27531390.20361670180998
3.01-3.080.28471640.2061553171798
3.08-3.150.31061310.1991699183098
3.15-3.230.28351450.2081630177599
3.23-3.310.2671380.18681655179398
3.31-3.410.22391510.18121618176999
3.41-3.520.25161430.16871669181298
3.52-3.650.29711240.17781683180799
3.65-3.790.23611520.16691648180098
3.79-3.970.24071430.16811663180699
3.97-4.170.1991340.14461652178698
4.18-4.440.18451300.13811643177398
4.44-4.780.2121570.14971617177499
4.78-5.260.24931350.17541672180798
5.26-6.010.25621510.21131650180198
6.02-7.570.24471340.20991661179598
7.57-36.190.18981490.171613176297

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