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- PDB-8etx: Ancestral PETase 55_547 -

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Basic information

Entry
Database: PDB / ID: 8etx
TitleAncestral PETase 55_547
ComponentsPolyethylene terephthalate hydrolase
KeywordsHYDROLASE / PET / PETase / Plastic degradation / Ancestral Sequence Reconstruction
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSaunders, J.W. / Frkic, R.L. / Jackson, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2025
Title: Ancestral reconstruction of polyethylene terephthalate degrading cutinases reveals a rugged and unexplored sequence-fitness landscape.
Authors: Vongsouthi, V. / Georgelin, R. / Matthews, D.S. / Saunders, J. / Lee, B.M. / Ton, J. / Damry, A.M. / Frkic, R.L. / Spence, M.A. / Jackson, C.J.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyethylene terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6589
Polymers30,0661
Non-polymers5928
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.166, 150.574, 55.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-303-

EDO

21A-306-

NA

31A-308-

CL

41A-566-

HOH

51A-572-

HOH

61A-581-

HOH

71A-634-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyethylene terephthalate hydrolase


Mass: 30066.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ancestral PETase 55_547 / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 286 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.1M Bis Tris Propane pH 7.5, 0.2M Potassium Sodium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.75→41.9 Å / Num. obs: 30223 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 24.61 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.053 / Rrim(I) all: 0.168 / Net I/σ(I): 9.1 / Num. measured all: 300463
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
1.75-1.7810.22.4221674316370.4420.7952.5511100
9.09-41.98.10.06520852570.9970.0240.0728.399.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QGC

6qgc


Resolution: 1.75→41.9 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 1547 5.12 %
Rwork0.1658 28662 -
obs0.1672 30209 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.79 Å2 / Biso mean: 29.5049 Å2 / Biso min: 15.3 Å2
Refinement stepCycle: final / Resolution: 1.75→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1965 0 64 278 2307
Biso mean--50.23 34.85 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.75-1.810.31851340.293725792713
1.81-1.870.31961460.265925362682
1.87-1.950.24331220.229325912713
1.95-2.030.19461490.196825842733
2.03-2.140.20581530.184125602713
2.14-2.280.20531410.170725842725
2.28-2.450.19261490.157925802729
2.45-2.70.19811500.16426042754
2.7-3.090.21311300.16226242754
3.09-3.890.16691400.143926462786
3.89-41.90.16451330.144127742907
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)
15.4911.2453-2.49363.3549-2.98056.1373-0.02840.1163-0.3502-0.1284-0.0302-0.12240.190.22690.05220.20980.0197-0.01080.1914-0.05740.111916.9619-0.55647.0384
20.9990.73070.16333.86661.4041.7073-0.0540.06550.2932-0.0455-0.04870.2743-0.1507-0.08140.10860.19720.0143-0.03140.19450.02270.21719.114818.09379.8103
34.43893.29142.19457.00992.1951.9772-0.1518-0.21180.51880.0347-0.09680.6431-0.1981-0.05660.2870.16340.00460.01930.1853-0.00020.23093.579915.011717.2799
43.83721.98340.27143.50360.20071.3240.0821-0.18440.2450.2821-0.14380.0833-0.1723-0.0210.05150.2450.0037-0.00890.1632-0.01330.175220.425218.874823.5333
52.80330.02940.09925.45780.30025.1380.0146-0.28940.10830.3383-0.1311-0.1642-0.17490.28120.14940.1607-0.0145-0.02350.1932-0.00080.166527.392113.546125.9018
62.71342.2119-0.46345.6303-0.74171.6532-0.0360.14920.2058-0.226-0.0507-0.0313-0.10790.11830.10230.18060.0024-0.010.20740.02390.154123.923313.203512.2673
74.3649-0.89321.90140.2367-0.33340.84210.01180.0831-0.1722-0.03110.0632-0.0263-0.01550.0756-0.05840.2315-0.01510.010.2588-0.02180.193331.1614-5.361817.435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 96 )A26 - 96
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 125 )A97 - 125
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 186 )A126 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 205 )A187 - 205
6X-RAY DIFFRACTION6chain 'A' and (resid 206 through 232 )A206 - 232
7X-RAY DIFFRACTION7chain 'A' and (resid 233 through 261 )A233 - 261

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