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- PDB-7xtr: The apo structure of the engineered TfCut -

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Basic information

Entry
Database: PDB / ID: 7xtr
TitleThe apo structure of the engineered TfCut
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / PETase / cutinase / enzyme engineering / PBAT degradation
Function / homology:
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYang, Y. / Jiang, P.C. / Huang, J.-W. / Chen, C.-C. / Guo, R.-T.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870790 China
National Natural Science Foundation of China (NSFC)31971205 China
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases.
Authors: Yang, Y. / Min, J. / Xue, T. / Jiang, P. / Liu, X. / Peng, R. / Huang, J.W. / Qu, Y. / Li, X. / Ma, N. / Tsai, F.C. / Dai, L. / Zhang, Q. / Liu, Y. / Chen, C.C. / Guo, R.T.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: alpha/beta hydrolase
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8517
Polymers56,4672
Non-polymers3835
Water6,089338
1
A: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5215
Polymers28,2341
Non-polymers2874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3302
Polymers28,2341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.689, 41.961, 80.767
Angle α, β, γ (deg.)90.000, 92.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha/beta hydrolase / Cutinase


Mass: 28233.678 Da / Num. of mol.: 2 / Mutation: H184S,F188I
Source method: isolated from a genetically manipulated source
Details: GB:PZN61876.1 / Source: (gene. exp.) Thermobifida fusca (bacteria) / Gene: cut-2.KW3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: cutinase
#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 273 K / Method: evaporation / pH: 8.5
Details: 20% w/v PEG3350, 0.2 M Sodium nitrate, 0.1 M BIS-Tris propane 8.5

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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: Nov 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.2→37.2 Å / Num. obs: 38580 / % possible obs: 96.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.1
Reflection shellResolution: 2.2→2.23 Å / Rmerge(I) obs: 0.099 / Mean I/σ(I) obs: 3 / Num. unique obs: 860

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Processing

Software
NameVersionClassification
SAINTdata scaling
PHENIX1.17refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CG2

4cg2


Resolution: 2.2→32.68 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2327 3542 9.18 %
Rwork0.1714 35038 -
obs0.1769 38580 88.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.45 Å2 / Biso mean: 16.2891 Å2 / Biso min: 3.78 Å2
Refinement stepCycle: final / Resolution: 2.2→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3919 0 23 338 4280
Biso mean--25.54 21.38 -
Num. residues----515
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.29381310.17241353148485
2.23-2.260.32331310.17661321145284
2.26-2.30.27251360.18591281141782
2.3-2.330.25351250.17171307143280
2.33-2.370.24081430.16481237138080
2.37-2.410.29531170.16461318143586
2.41-2.450.27521330.18941408154184
2.45-2.50.25861440.18111312145686
2.5-2.550.29511430.21364150786
2.55-2.610.32091390.18941431157086
2.61-2.670.30461310.19591362149389
2.67-2.740.24781400.18551490163093
2.74-2.810.25351590.19041455161491
2.81-2.890.2811580.2051468162693
2.89-2.990.32891390.18831497163692
2.99-3.090.24441500.18221420157093
3.09-3.220.27181420.18511501164392
3.22-3.360.21981370.17021458159593
3.36-3.540.24311450.17411481162691
3.54-3.760.19571420.15961409155189
3.76-4.050.17291470.1461400154790
4.05-4.460.15641480.13721429157790
4.46-5.10.17621500.1441454160491
5.1-6.420.20611550.17881438159392
6.42-32.680.17711570.16391444160191

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