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- PDB-8j5n: Crystal structure of a PETase variant V20 from Ideonella sakaiensis -

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Basic information

Entry
Database: PDB / ID: 8j5n
TitleCrystal structure of a PETase variant V20 from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / plastic degradation / PET / mutant
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
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWei, H.L. / Gao, S.F. / Li, Q. / Liu, W.D. / Zhu, L.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Engineering (Beijing) / Year: 2024
Title: beta-sheet Engineering of IsPETase for PET Depolymerization
Authors: Gao, S. / Shi, L. / Wei, H. / Liu, P. / Zhao, W. / Gong, L. / Tan, Z. / Zhai, H. / Liu, W. / Liu, H. / Zhu, L.
History
DepositionApr 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
D: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)62,7502
Polymers62,7502
Non-polymers00
Water3,765209
1
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)31,3751
Polymers31,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)31,3751
Polymers31,3751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.279, 77.925, 125.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11D-365-

HOH

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 31374.971 Da / Num. of mol.: 2 / Mutation: V14E,L18P,R53Q,V84L,D186H,F201I,F209Y,N233K,R280E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
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: 1.96 Å3/Da / Density % sol: 37.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 8% Tacsimate pH 5.0, 20% Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→48.81 Å / Num. obs: 32014 / % possible obs: 99.3 % / Redundancy: 10 % / CC1/2: 0.993 / Net I/σ(I): 6.2
Reflection shellResolution: 1.95→2.07 Å / Redundancy: 8.1 % / Num. unique obs: 4930 / CC1/2: 0.745 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XH3

5xh3


Resolution: 2→48.81 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.755 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27841 1585 4.8 %RANDOM
Rwork0.22557 ---
obs0.22813 31578 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.04 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3834 0 0 209 4043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133928
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183572
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.6435354
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5718230
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5525520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13121.724174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6815578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8641524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024592
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02928
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4431.9962086
X-RAY DIFFRACTIONr_mcbond_other1.4381.9952085
X-RAY DIFFRACTIONr_mcangle_it2.2162.9842604
X-RAY DIFFRACTIONr_mcangle_other2.2172.9852605
X-RAY DIFFRACTIONr_scbond_it1.7832.1911842
X-RAY DIFFRACTIONr_scbond_other1.7812.1911842
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8063.222751
X-RAY DIFFRACTIONr_long_range_B_refined4.58124.4714438
X-RAY DIFFRACTIONr_long_range_B_other4.58224.4674438
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 114 -
Rwork0.305 2173 -
obs--92.4 %

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