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- PDB-8ety: Ancestral PETase 35_442 -

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Basic information

Entry
Database: PDB / ID: 8ety
TitleAncestral PETase 35_442
ComponentsPolyethylene terephthalate hydrolase
KeywordsHYDROLASE / PET / PETase / Plastic degradation / Ancestral Sequence Reconstruction
Function / homologyDI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsSaunders, J.W. / Frkic, R.L. / Jackson, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Ancestral PETase 35_442
Authors: Saunders, J. / Frkic, R.L. / Jackson, C.J.
History
DepositionOct 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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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)31,41215
Polymers30,2531
Non-polymers1,15814
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.759, 148.498, 55.554
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-304-

EDO

21A-416-

HOH

31A-523-

HOH

41A-594-

HOH

51A-595-

HOH

61A-596-

HOH

71A-629-

HOH

81A-641-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyethylene terephthalate hydrolase


Mass: 30253.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Ancestral PETase 35_442 / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 336 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.1M Bis Tris Propane pH 6.5, 0.2M Sodium malonate

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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: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.54→40.37 Å / Num. obs: 43143 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 20.45 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.054 / Rrim(I) all: 0.196 / Net I/σ(I): 10.6 / Num. measured all: 559191 / Scaling rejects: 2349
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
1.54-1.5713.45.9882819921120.3851.7156.2321100
8.44-40.3711.30.06435373120.9980.0190.06734.198.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QGC

6qgc


Resolution: 1.54→40.37 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2102 4.88 %
Rwork0.1694 40969 -
obs0.1709 43071 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.04 Å2 / Biso mean: 26.1538 Å2 / Biso min: 11.82 Å2
Refinement stepCycle: final / Resolution: 1.54→40.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 74 322 2365
Biso mean--49.14 38.33 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.54-1.580.29681240.28232666279099
1.58-1.620.2611410.259227002841100
1.62-1.660.27651460.255126802826100
1.66-1.710.2871410.248227132854100
1.71-1.760.28581430.249326672810100
1.76-1.830.24151310.208527322863100
1.83-1.90.23991520.183626922844100
1.9-1.990.20221330.173927262859100
1.99-2.090.19011350.169627242859100
2.09-2.220.20181200.158927442864100
2.22-2.390.18011500.156327192869100
2.39-2.630.22391310.159727662897100
2.63-3.010.19441560.169827382894100
3.01-3.80.17771430.147427922935100
3.8-40.370.16731560.14929103066100
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)
13.974-0.8529-1.44321.7847-1.24455.62-0.00920.056-0.272-0.1193-0.05460.08140.19940.08920.04790.1612-0.0088-0.02190.1338-0.04020.108716.6175-0.95977.0608
21.0193-0.8869-0.11452.18112.41353.81260.0690.16330.2277-0.5999-0.38390.3358-0.5876-0.53570.20170.24750.0367-0.06830.2115-0.00920.35181.763922.05919.3047
32.33231.20320.17222.8804-0.48543.5191-0.12710.13860.0723-0.318-0.0141-0.00560.2563-0.08980.12940.1657-0.0213-0.00640.1764-0.01020.16585.46096.33915.6905
41.24690.65140.11042.93270.64391.818-0.03940.03940.3237-0.0327-0.06820.2647-0.31320.02930.08790.1733-0.0111-0.04950.1350.01530.205612.869321.08711.5232
53.17792.18610.95244.42121.23481.1464-0.1586-0.03670.34940.0241-0.01130.6651-0.1118-0.07160.21190.17520.01210.00060.17330.01760.26583.203714.610516.8753
61.04080.0760.19042.0930.06660.9823-0.0116-0.03080.10910.0982-0.05950.0187-0.11490.10540.06650.1451-0.0312-0.01540.15770.00860.114322.503313.949820.3502
72.59841.6174.40162.92224.20098.68140.0098-0.02330.124-0.1726-0.03020.1071-0.3404-0.3889-0.04630.1759-0.02110.03190.2913-0.03070.181837.5271-8.585919.3217
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 41 )A26 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 56 )A42 - 56
4X-RAY DIFFRACTION4chain 'A' and (resid 57 through 96 )A57 - 96
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 125 )A97 - 125
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 248 )A126 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 261 )A249 - 261

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