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- PDB-8eu1: Ancestral PETase 35_442 Mutant F93L -

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Basic information

Entry
Database: PDB / ID: 8eu1
TitleAncestral PETase 35_442 Mutant F93L
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: 2.23 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 Mutant F93L
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)30,5778
Polymers30,0881
Non-polymers4887
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.920, 148.624, 55.893
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-416-

HOH

21A-426-

HOH

31A-464-

HOH

41A-478-

HOH

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Components

#1: Protein Polyethylene terephthalate hydrolase


Mass: 30088.240 Da / Num. of mol.: 1 / Mutation: F93L
Source method: isolated from a genetically manipulated source
Details: Ancestral PETase 35_442 Mutant F93L / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3350, 0.1M Bis Tris propane pH 6.5, 0.2M Sodium potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 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: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.23→63.27 Å / Num. obs: 14586 / % possible obs: 99.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 23.16 Å2 / CC1/2: 0.644 / Rmerge(I) obs: 1.086 / Rpim(I) all: 0.348 / Rrim(I) all: 1.146 / Net I/σ(I): 4.8 / Num. measured all: 183624 / Scaling rejects: 9193
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
2.23-2.39.76.6631270113070.4192.7087.2771.199.3
8.92-63.2711.70.11132182750.9850.0370.11715.699.8

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QGC

6qgc


Resolution: 2.23→63.27 Å / SU ML: 0.62 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2941 675 4.8 %
Rwork0.2432 13402 -
obs0.2457 14077 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.16 Å2 / Biso mean: 30.2857 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: final / Resolution: 2.23→63.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 31 78 2067
Biso mean--42.2 30.45 -
Num. residues----260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.23-2.40.60171160.55972376249287
2.4-2.640.40091400.37552589272995
2.64-3.030.32821400.269127402880100
3.03-3.810.27911280.187727942922100
3.81-63.270.18321510.142129033054100
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)
11.5197-0.59430.0131.1269-0.32171.12990.0231-0.0365-0.3816-0.346-0.05810.0160.2170.3249-0.08010.3042-0.0004-0.01510.4614-0.05610.273617.31830.13356.8277
21.33191.02560.57031.15870.10281.1230.01380.09060.6281-0.2213-0.05550.1465-0.327-0.5709-0.01630.25750.1139-0.05390.330.0850.33021.841622.14079.3575
30.92510.3204-0.5162.7512-1.10381.2493-0.11110.14470.0564-0.71210.0864-0.18360.2021-0.23050.05880.2370.0654-0.02560.2052-0.11310.1825.6117.16795.7797
40.59810.33750.12510.9556-0.42760.5722-0.14660.1620.2048-0.31120.24530.092-0.06370.20660.0030.27610.055-0.02680.2679-0.0250.280712.943420.775311.5228
51.64091.11860.19491.3891-0.19620.91610.1591-0.35510.21110.3899-0.05810.2409-0.2339-0.2174-0.01180.26450.0617-0.03130.1529-0.00330.32397.646116.647519.161
61.264-0.05030.13690.98760.60471.23420.0231-0.13560.11670.10780.11410.00270.03950.1256-0.08170.27660.0014-0.01380.23120.01510.23824.138113.108319.8982
71.37910.82570.65281.81180.71491.36820.1775-0.19950.29610.1305-0.34130.3729-0.0671-0.0201-0.06340.30640.10750.10390.4559-0.07370.288837.936-8.118419.3798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A2 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 41 )A26 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 55 )A42 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 96 )A56 - 96
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 144 )A97 - 144
6X-RAY DIFFRACTION6chain 'A' and (resid 145 through 248 )A145 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 261 )A249 - 261

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