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- PDB-7xts: The apo structure of the engineered TfCut S130A -

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Basic information

Entry
Database: PDB / ID: 7xts
TitleThe apo structure of the engineered TfCut S130A
Componentsalpha/beta hydrolase
KeywordsHYDROLASE / PETase / cutinase / enzyme engineering / PBAT degradation
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 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)32101016 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)56,4814
Polymers56,4352
Non-polymers462
Water6,215345
1
A: alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)28,2181
Polymers28,2181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2643
Polymers28,2181
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.025, 42.959, 80.377
Angle α, β, γ (deg.)90.000, 92.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alpha/beta hydrolase / Cutinase


Mass: 28217.678 Da / Num. of mol.: 2 / Mutation: S130A,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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 30% W/V PEG8000; 0.2 M Ammonium sulfate; 0.1 M Sodium cacodylate 6.5

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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 III / Detector: PIXEL / Date: Nov 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 2.21→37.88 Å / Num. obs: 43207 / % possible obs: 99.4 % / Redundancy: 4.78 % / Rmerge(I) obs: 0.1199 / Net I/σ(I): 8.53
Reflection shellResolution: 2.21→2.24 Å / Redundancy: 4.78 % / Rmerge(I) obs: 0.2431 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 882 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SADABSdata scaling
PHENIX1.17.1refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZOA

5zoa


Resolution: 2.21→34.94 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2371 3759 8.7 %
Rwork0.179 39448 -
obs0.1839 43207 97.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.52 Å2 / Biso mean: 21.7128 Å2 / Biso min: 9.89 Å2
Refinement stepCycle: final / Resolution: 2.21→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 2 345 4321
Biso mean--19.81 25.98 -
Num. residues----522
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 (%)
2.21-2.240.32751320.24541326145891
2.24-2.270.31421340.24321405153991
2.27-2.30.3241430.24541350149393
2.3-2.330.30111260.25491405153194
2.33-2.370.27191310.22261458158996
2.37-2.40.29691560.23831443159997
2.4-2.440.30121200.22791468158899
2.44-2.480.32681500.22351493164399
2.48-2.530.28171470.21721494164199
2.53-2.580.27251490.20311420156999
2.58-2.630.2531330.206815291662100
2.63-2.690.27731450.20961472161799
2.69-2.750.3381320.22791450158299
2.75-2.820.3171460.20971490163699
2.82-2.90.30691340.21331487162199
2.9-2.980.27781470.20321488163599
2.98-3.080.26291460.191504165099
3.08-3.190.24511450.18314551600100
3.19-3.310.21151370.173915091646100
3.31-3.470.23111430.16521473161699
3.47-3.650.22161430.15881483162699
3.65-3.880.21081350.13981482161798
3.88-4.170.17761390.14161461160098
4.17-4.590.13791280.11741473160198
4.59-5.260.18641420.12441496163899
5.26-6.620.19171510.15631464161599
6.62-34.940.12771250.15011470159597

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