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- PDB-8h83: Crystal structure of a IsPETase variant V22 from Ideonella sakaiensis -

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Basic information

Entry
Database: PDB / ID: 8h83
TitleCrystal structure of a IsPETase variant V22 from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET degradation / 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
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: 1.92 Å
AuthorsWei, H.L. / Gao, S.F. / Li, Q. / Han, X. / Gao, J. / Liu, W.D.
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
DepositionOct 21, 2022Deposition 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
B: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)69,2702
Polymers69,2702
Non-polymers00
Water8,161453
1
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)34,6351
Polymers34,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)34,6351
Polymers34,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.234, 80.656, 134.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-520-

HOH

31A-527-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 62 through 321)
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYHOHHOH(chain A and resid 62 through 321)AA - C62 - 32194
2ASNASNCYSCYSchain BBB30 - 28962 - 321

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Components

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


Mass: 34634.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Gene: ISF6_4831 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.01 Å3/Da / Density % sol: 38.8 % / Mosaicity: 0.851 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.0 M sodium citrate, 0.1 M Imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2022
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 43072 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 23.79 Å2 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.062 / Rrim(I) all: 0.227 / Χ2: 0.959 / Net I/σ(I): 3.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.93-28.71.51642200.5480.5381.6150.79299.4
2-2.0811.71.10242140.8040.3361.1540.85899.9
2.08-2.1713.40.86742520.90.2450.9020.92100
2.17-2.2913.50.66742580.9340.1880.6941.075100
2.29-2.4313.40.51142690.9560.1440.5311.022100
2.43-2.6213.90.39842690.9760.110.4130.984100
2.62-2.8813.70.27543180.9870.0760.2860.963100
2.88-3.313.80.17643110.9940.0490.1830.933100
3.3-4.16140.10343750.9970.0280.1070.858100
4.16-5013.80.07245860.9990.020.0751.1100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XH3

5xh3


Resolution: 1.92→47.89 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 2098 5 %
Rwork0.1922 39858 -
obs0.193 41956 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.01 Å2 / Biso mean: 24.4271 Å2 / Biso min: 12.09 Å2
Refinement stepCycle: final / Resolution: 1.92→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 0 453 4285
Biso mean---33.75 -
Num. residues----521
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1579X-RAY DIFFRACTION1.319TORSIONAL
12B1579X-RAY DIFFRACTION1.319TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.92-1.990.36081510.32282875302671
1.99-2.070.27732080.25513936414497
2.07-2.160.27122130.227540324245100
2.16-2.280.2392130.210240584271100
2.28-2.420.24182140.199340804294100
2.42-2.610.20152160.186741144330100
2.61-2.870.21262170.178241044321100
2.87-3.290.17812170.176241254342100
3.29-4.140.18122200.166941834403100
4.14-47.890.18292290.186443514580100

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