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- PDB-7w5g: The apo structure of trichobrasilenol synthase TaTC6 with the spa... -

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Basic information

Entry
Database: PDB / ID: 7w5g
TitleThe apo structure of trichobrasilenol synthase TaTC6 with the space group of orthorhombic
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 / 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
Biological speciesHypocrea atroviridis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9744
Polymers45,6901
Non-polymers2843
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area16270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.831, 71.063, 81.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Terpene cyclase 6 / Sesquiterpene synthase 6


Mass: 45690.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea atroviridis (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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 297 K / Method: evaporation
Details: 1.6 M Lithium sulfate, 0.09 M Magnesium sulfate, 50 mM HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 36792 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.036 / Rrim(I) all: 0.101 / Χ2: 0.698 / Net I/σ(I): 5.7 / Num. measured all: 287793
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.867.10.4836040.9220.1920.5180.30499.9
1.86-1.947.80.3636180.960.1380.3860.346100
1.94-2.0380.26236430.980.10.280.388100
2.03-2.1380.19436300.9860.0740.2080.471100
2.13-2.278.10.14936390.9910.0560.160.54100
2.27-2.448.10.12336700.9930.0470.1320.581100
2.44-2.6980.09736580.9960.0370.1040.648100
2.69-3.0880.07937070.9970.030.0840.82100
3.08-3.877.80.07637120.9960.030.0821.67299.9
3.87-257.50.0539110.9980.020.0541.164100

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4okm

4okm


Resolution: 1.8→23.66 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 2005 5.46 %
Rwork0.1579 34692 -
obs0.1598 36697 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.58 Å2 / Biso mean: 20.6712 Å2 / Biso min: 4.29 Å2
Refinement stepCycle: final / Resolution: 1.8→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 16 472 3402
Biso mean--34.12 28.57 -
Num. residues----355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.850.23911410.21142394253598
1.85-1.90.21391430.175424482591100
1.9-1.950.17991330.153824472580100
1.95-2.020.20991460.150624622608100
2.02-2.090.20461410.150624492590100
2.09-2.170.18711320.152424572589100
2.17-2.270.18781540.147124542608100
2.27-2.390.2111360.150524812617100
2.39-2.540.20481430.163824682611100
2.54-2.740.19241420.162824772619100
2.74-3.010.20161480.16224902638100
3.01-3.440.19551440.158425072651100
3.45-4.340.17041440.138125262670100
4.34-23.660.18721580.17062632279099

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