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- PDB-8gu5: Wild type poly(ethylene terephthalate) hydrolase -

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Basic information

Entry
Database: PDB / ID: 8gu5
TitleWild type poly(ethylene terephthalate) hydrolase
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / LYASE
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / 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: 2.02 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

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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)28,7831
Polymers28,7831
Non-polymers00
Water2,864159
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)51.438, 55.454, 85.458
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: 28782.916 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 / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 7.5
Details: 0.2 M Calcium chloride dihydrate, 0.1 M HEPES sodium pH 7.5, 28 % v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16412 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 28.71 Å2 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.09 / Rrim(I) all: 0.174 / Χ2: 1.978 / Net I/σ(I): 5.3 / Num. measured all: 90297
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2-2.035.58090.6550.5821.11499.9
2.03-2.075.67980.6670.5281.12499.9
2.07-2.115.68110.6420.4691.159100
2.11-2.155.77950.7670.4021.2031000.8880.976
2.15-2.25.68140.740.4371.37499.90.948
2.2-2.254.88050.6680.4622.1799.40.923
2.25-2.315.27990.8280.3351.4681000.6920.771
2.31-2.375.28170.830.2481.3461000.5080.567
2.37-2.445.58070.8850.2051.46399.90.4420.488
2.44-2.5268070.9280.1691.5091000.3860.422
2.52-2.6168190.9390.1551.4671000.3490.383
2.61-2.7168180.940.131.7071000.2920.32
2.71-2.845.98140.9580.1171.75199.90.2620.288
2.84-2.995.88250.9640.0951.9851000.2090.231
2.99-3.175.68230.9750.0832.32499.90.1790.198
3.17-3.4258250.9750.0772.6999.40.1550.174
3.42-3.765.48240.9760.063.03199.90.1260.14
3.76-4.315.68390.9850.053.39298.90.1070.119
4.31-5.435.28420.990.0493.60698.20.0980.11
5.43-504.89210.9920.0453.96999.70.0890.1

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 2.02→46.52 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 841 5.14 %
Rwork0.179 15526 -
obs0.1812 16367 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.69 Å2 / Biso mean: 30.224 Å2 / Biso min: 15.83 Å2
Refinement stepCycle: final / Resolution: 2.02→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 0 159 2093
Biso mean---37.8 -
Num. residues----263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.150.28291260.22452391251792
2.15-2.310.28611160.214225942710100
2.31-2.550.26771420.193725862728100
2.55-2.910.2531500.181226072757100
2.91-3.670.19391330.170926312764100
3.67-46.520.19211740.16392717289199
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)
11.9594-0.2714-0.62141.70461.01322.3005-0.0288-0.0128-0.16710.0747-0.0372-0.05860.23410.11680.07550.1872-0.0026-0.00880.1540.02540.202847.509520.784643.1038
22.245-0.90550.12263.66460.72311.3127-0.0019-0.01640.04910.1521-0.06590.1416-0.0383-0.28270.07540.1884-0.00120.01660.20450.00280.13137.846431.037843.8301
35.0372-2.80621.59643.9757-1.87012.79060.06760.3803-0.0110.054-0.09660.0247-0.14030.36590.04970.171-0.02990.02250.2286-0.02210.136348.51337.070445.6123
41.00460.11280.21781.1413-0.23772.4382-0.05420.06750.0284-0.00020.0560.07180.0034-0.09990.01690.22340.00480.01780.2075-0.00910.225540.676733.947232.1237
55.8133-1.1075-0.22361.4264-0.40041.31360.19740.1924-0.0855-0.0069-0.1294-0.10050.12390.154-0.09670.20650.00110.00450.1662-0.04140.188845.798820.440129.2235
67.12721.0025-0.55275.8919-0.44433.14650.0963-0.1748-0.0561-0.25610.031-0.10180.28540.0157-0.16340.28580.00950.02450.3235-0.060.23536.925124.123520.0602
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 58 )A2 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 93 )A59 - 93
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 113 )A94 - 113
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 220 )A114 - 220
5X-RAY DIFFRACTION5chain 'A' and (resid 221 through 247 )A221 - 247
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 264 )A248 - 264

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