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- PDB-8j17: Crystal structure of IsPETase variant -

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Basic information

Entry
Database: PDB / ID: 8j17
TitleCrystal structure of IsPETase variant
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / polyethylene terephthalate (PET) / IsPETase / PET degradation
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / 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: 1.97 Å
AuthorsYin, Q.D. / Wang, Y.X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21621004 China
National Natural Science Foundation of China (NSFC)22078239 China
CitationJournal: Green Chem / Year: 2013
Title: Efficient polyethylene terephthalate biodegradation by an engineered Ideonella sakaiensis PETase with a fixed substrate-binding W156 residue
Authors: Yin, Q. / Zhang, J. / Ma, S. / Gu, T. / Wang, M. / You, S. / Ye, S. / Su, R. / Wang, Y. / Qi, W.
History
DepositionApr 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
B: Poly(ethylene terephthalate) hydrolase
C: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)86,2473
Polymers86,2473
Non-polymers00
Water13,709761
1
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)28,7491
Polymers28,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)28,7491
Polymers28,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)28,7491
Polymers28,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.560, 233.800, 163.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-474-

HOH

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Components

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


Mass: 28748.943 Da / Num. of mol.: 3
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.: 761 / 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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100mM MES-NaOH, 1.7M MgSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→58.45 Å / Num. obs: 71765 / % possible obs: 99.8 % / Redundancy: 11.4 % / Biso Wilson estimate: 37.3 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.7
Reflection shellResolution: 1.97→2.02 Å / Num. unique obs: 5267 / CC1/2: 0.672

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PRODDdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→40.92 Å / SU ML: 0.216 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9067
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 3529 4.92 %
Rwork0.1755 68176 -
obs0.1774 71705 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.91 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5770 0 0 761 6531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665908
X-RAY DIFFRACTIONf_angle_d0.82358054
X-RAY DIFFRACTIONf_chiral_restr0.0538888
X-RAY DIFFRACTIONf_plane_restr0.00631066
X-RAY DIFFRACTIONf_dihedral_angle_d16.46052092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-20.35431500.33092676X-RAY DIFFRACTION99.19
2-2.030.34091410.30842713X-RAY DIFFRACTION99.62
2.03-2.060.27951400.28022653X-RAY DIFFRACTION99.75
2.06-2.090.34441500.272687X-RAY DIFFRACTION99.72
2.09-2.120.29411560.24482675X-RAY DIFFRACTION99.72
2.12-2.160.2791380.23832680X-RAY DIFFRACTION99.89
2.16-2.20.28341460.22472719X-RAY DIFFRACTION99.72
2.2-2.240.26131350.21382681X-RAY DIFFRACTION99.58
2.24-2.290.25391310.20762747X-RAY DIFFRACTION99.97
2.29-2.340.23921520.19152654X-RAY DIFFRACTION99.86
2.34-2.390.25171280.19052770X-RAY DIFFRACTION99.83
2.39-2.450.24891200.18622682X-RAY DIFFRACTION99.86
2.45-2.520.23051320.19552742X-RAY DIFFRACTION99.76
2.52-2.590.25531350.18712697X-RAY DIFFRACTION99.86
2.59-2.670.21151330.19312731X-RAY DIFFRACTION99.79
2.67-2.770.24831450.19382734X-RAY DIFFRACTION99.79
2.77-2.880.26381380.20762708X-RAY DIFFRACTION99.96
2.88-3.010.2711220.19912725X-RAY DIFFRACTION99.65
3.01-3.170.22561390.19112758X-RAY DIFFRACTION99.86
3.17-3.370.21540.18062719X-RAY DIFFRACTION100
3.37-3.630.2211560.16322751X-RAY DIFFRACTION100
3.63-3.990.17621520.13782759X-RAY DIFFRACTION99.79
3.99-4.570.16881450.13132771X-RAY DIFFRACTION100
4.57-5.750.15551490.14022810X-RAY DIFFRACTION99.83
5.76-40.920.18821420.15992934X-RAY DIFFRACTION99.29

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