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- PDB-7xtw: The structure of IsPETase in complex with MHET -

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Basic information

Entry
Database: PDB / ID: 7xtw
TitleThe structure of IsPETase in complex with MHET
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / PBAT hydrolase / enzyme engineering
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-(2-hydroxyethyloxycarbonyl)benzoic acid / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 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 16, 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: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,36310
Polymers27,3661
Non-polymers9979
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-55 kcal/mol
Surface area9700 Å2
Unit cell
Length a, b, c (Å)50.836, 50.889, 84.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Poly(ethylene terephthalate) hydrolase / PETase


Mass: 27366.400 Da / Num. of mol.: 1 / Mutation: R132G,S160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: 201-F6 / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 1.99 Å3/Da / Density % sol: 38.11 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8
Details: 1.6 M Ammonium Sulfate; 0.1 M Tris pH 8.0; 15% glycerol

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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: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.91→35.97 Å / Num. obs: 32588 / % possible obs: 99.8 % / Redundancy: 6.12 % / Rmerge(I) obs: 0.0525 / Net I/σ(I): 22.91
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 5.47 % / Rmerge(I) obs: 0.1421 / Mean I/σ(I) obs: 9.5 / Num. unique obs: 762 / CC1/2: 0.984 / % possible all: 98.3

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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: 5XG0

5xg0


Resolution: 1.91→35.97 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 11.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1494 3285 10.08 %
Rwork0.1359 29303 -
obs0.1372 32588 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.63 Å2 / Biso mean: 13.1083 Å2 / Biso min: 1.85 Å2
Refinement stepCycle: final / Resolution: 1.91→35.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 60 253 2224
Biso mean--34.47 24.72 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.940.18151450.15721224136997
1.94-1.970.15621400.13611260140099
1.97-20.15561440.13112971441100
2-2.040.15631440.121412861430100
2.04-2.070.15161400.141112171357100
2.07-2.110.16231500.138913281478100
2.11-2.160.17451410.131512281369100
2.16-2.20.16311480.131813041452100
2.2-2.250.14991290.129612671396100
2.25-2.310.11361500.129213131463100
2.31-2.370.15171320.132912281360100
2.37-2.440.15421490.131512981447100
2.44-2.520.19491460.134412941440100
2.52-2.610.19551280.143912471375100
2.61-2.720.17251440.137713091453100
2.72-2.840.15541510.146212821433100
2.84-2.990.13971460.138513031449100
2.99-3.180.14751430.129612501393100
3.18-3.420.1251370.12912861423100
3.42-3.760.1211420.11912561398100
3.77-4.310.13331360.122312871423100
4.31-5.420.13891560.132712651421100
5.43-35.970.15021440.19091274141899

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