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- PDB-5yfe: Enzymatic and structural characterization of the poly (ethylene t... -

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Basic information

Entry
Database: PDB / ID: 5yfe
TitleEnzymatic and structural characterization of the poly (ethylene terephthalate) hydrolase PETase from I. sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET degradation
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / 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
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsBao, R. / He, L.H. / Liu, B.
CitationJournal: Chembiochem / Year: 2018
Title: Protein Crystallography and Site-Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from Ideonella sakaiensis.
Authors: Liu, B. / He, L. / Wang, L. / Li, T. / Li, C. / Liu, H. / Luo, Y. / Bao, R.
History
DepositionSep 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0695
Polymers28,6931
Non-polymers3764
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.945, 56.644, 80.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28692.705 Da / Num. of mol.: 1 / Mutation: T46N, R198A, A261N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria)
Strain: 201-F6 / Gene: ISF6_4831 / Plasmid: pET-21(b) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 25%PEG 4000, Sodium acetate pH 4.6, 0.2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.39→37.88 Å / Num. obs: 47656 / % possible obs: 99.99 % / Redundancy: 14.1 % / Net I/σ(I): 17.39
Reflection shellResolution: 1.39→1.44 Å / Num. unique obs: 4675 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LUI

5lui


Resolution: 1.39→37.879 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.2348 2000 4.2 %
Rwork0.2228 --
obs0.2233 47650 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.39→37.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1975 0 22 69 2066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0242042
X-RAY DIFFRACTIONf_angle_d2.0162778
X-RAY DIFFRACTIONf_dihedral_angle_d13.155718
X-RAY DIFFRACTIONf_chiral_restr0.114302
X-RAY DIFFRACTIONf_plane_restr0.012367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.42480.27121400.26263209X-RAY DIFFRACTION100
1.4248-1.46330.28921410.2453207X-RAY DIFFRACTION100
1.4633-1.50630.24381400.23553191X-RAY DIFFRACTION100
1.5063-1.5550.23771430.23113256X-RAY DIFFRACTION100
1.555-1.61050.24891400.22943216X-RAY DIFFRACTION100
1.6105-1.6750.24451420.22683223X-RAY DIFFRACTION100
1.675-1.75130.25011410.22443227X-RAY DIFFRACTION100
1.7513-1.84360.19891420.22963233X-RAY DIFFRACTION100
1.8436-1.95910.24651430.22883271X-RAY DIFFRACTION100
1.9591-2.11030.26031430.23333256X-RAY DIFFRACTION100
2.1103-2.32270.25621430.23363267X-RAY DIFFRACTION100
2.3227-2.65870.24491440.23033291X-RAY DIFFRACTION100
2.6587-3.34940.24971450.23173329X-RAY DIFFRACTION100
3.3494-37.89270.17961530.1823474X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.2139 Å / Origin y: 57.8608 Å / Origin z: 6.7276 Å
111213212223313233
T0.0543 Å20.0046 Å20.0051 Å2-0.0422 Å2-0.0035 Å2--0.055 Å2
L0.3364 °20.1202 °2-0.1306 °2-0.4652 °2-0.0994 °2--0.9192 °2
S-0.0269 Å °-0.0137 Å °-0.0403 Å °-0.001 Å °0.007 Å °-0.0507 Å °0.1824 Å °0.0056 Å °0.0047 Å °
Refinement TLS groupSelection details: all

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