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- PDB-8gu4: Poly(ethylene terephthalate) hydrolase (IsPETase)-linker -

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Basic information

Entry
Database: PDB / ID: 8gu4
TitlePoly(ethylene terephthalate) hydrolase (IsPETase)-linker
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / LYASE
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, 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: 1.5 Å
AuthorsXiao, Y.J. / Wang, Z.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970048 China
CitationJournal: Nat Commun / Year: 2022
Title: Biodegradation of highly crystallized poly(ethylene terephthalate) through cell surface codisplay of bacterial PETase and hydrophobin.
Authors: Chen, Z. / Duan, R. / Xiao, Y. / Wei, Y. / Zhang, H. / Sun, X. / Wang, S. / Cheng, Y. / Wang, X. / Tong, S. / Yao, Y. / Zhu, C. / Yang, H. / Wang, Y. / Wang, Z.
History
DepositionSep 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 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


Theoretical massNumber of molelcules
Total (without water)29,4131
Polymers29,4131
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.790, 59.940, 77.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29413.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria)
Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Gene: ISF6_4831 / 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.: 393 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 289 K / Method: batch mode
Details: 10 % w/v PEG 8000, 100 mM MES, Sodium Hydroxide, pH 6.0 200 mM Zinc Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97864 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97864 Å / Relative weight: 1
ReflectionResolution: 1.5→42.46 Å / Num. obs: 37971 / % possible obs: 98.6 % / Redundancy: 12.2 % / Biso Wilson estimate: 10.34 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.061 / Rrim(I) all: 0.213 / Net I/σ(I): 14.4 / Num. measured all: 463797 / Scaling rejects: 12243
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.549.70.7582584026650.8660.2490.8014.195.3
6.71-42.4611.80.05259955070.9970.0160.05527.799.6

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.5→27.95 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1896 1818 4.8 %
Rwork0.1572 36095 -
obs0.1587 37913 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.38 Å2 / Biso mean: 15.0456 Å2 / Biso min: 0.05 Å2
Refinement stepCycle: final / Resolution: 1.5→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 0 393 2349
Biso mean---27.13 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.540.26941420.20762629277195
1.54-1.590.20241460.18182685283197
1.59-1.640.19371400.17022721286198
1.64-1.70.2081500.16952711286198
1.7-1.760.22091290.1672762289198
1.76-1.840.19751320.16492744287699
1.84-1.940.18371220.16412775289799
1.94-2.060.19611350.16422772290798
2.06-2.220.19341490.16072788293799
2.22-2.440.20271400.16432808294899
2.45-2.80.18421410.164228352976100
2.8-3.520.21111360.147128763012100
3.53-27.950.13891560.1329893145100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.72790.0634-0.1610.64560.36440.25980.02480.19310.2847-0.03050.13450.1465-0.265-0.2303-0.01030.20850.05520.0420.15670.09120.22410.013513.4802-3.8723
21.8253-0.33030.23861.40760.08711.6826-0.019-0.07760.14680.18940.0320.0035-0.1129-0.1212-0.02230.08640.00470.02410.0857-0.01030.06311.9206-0.58899.6757
31.0719-0.4762-0.2341.6394-0.11350.9653-0.00140.010.06220.0630.0123-0.0537-0.04620.0839-0.0050.065-0.0018-0.00430.07670.0060.06510.0256-4.86392.0061
41.5195-0.7121-0.69171.15270.42171.619-0.03370.0349-0.01330.07070.0060.05840.097-0.1220.01750.0715-0.0147-0.00610.08360.01110.08060.2995-11.07023.4177
51.0724-0.15690.40670.9873-0.32063.42770.0335-0.06980.16050.18710.07410.1674-0.162-0.3032-0.05190.1020.01320.02140.14140.00680.122-7.08560.2158.6854
60.6234-0.0185-0.17970.6896-0.05661.09920.04080.1040.0565-0.0644-0.0024-0.0274-0.0375-0.0048-0.03630.0783-0.0019-0.00020.0890.02050.08298.1457-3.5354-11.7849
73.142-0.52590.43111.3674-0.25550.55530.06710.01580.1926-0.1568-0.1164-0.1087-0.08090.00660.05360.16760.00870.0280.15590.05230.12388.71856.1488-20.8334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )A1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 52 )A25 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 92 )A53 - 92
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 112 )A93 - 112
5X-RAY DIFFRACTION5chain 'A' and (resid 113 through 126 )A113 - 126
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 246 )A127 - 246
7X-RAY DIFFRACTION7chain 'A' and (resid 247 through 269 )A247 - 269

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