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- PDB-8eu0: Ancestral PETase 35_442 Mutant E27Q -

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Basic information

Entry
Database: PDB / ID: 8eu0
TitleAncestral PETase 35_442 Mutant E27Q
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: 2.06 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 E27Q
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
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyethylene terephthalate hydrolase
B: Polyethylene terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,94614
Polymers60,2752
Non-polymers67212
Water4,792266
1
A: Polyethylene terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4767
Polymers30,1371
Non-polymers3386
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyethylene terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4707
Polymers30,1371
Non-polymers3336
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.372, 68.372, 214.014
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polyethylene terephthalate hydrolase


Mass: 30137.271 Da / Num. of mol.: 2 / Mutation: E27Q
Source method: isolated from a genetically manipulated source
Details: Ancestral PETase 35_442 Mutant E27Q / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 278 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Sodium fluoride

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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: Apr 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.06→59.21 Å / Num. obs: 36969 / % possible obs: 100 % / Redundancy: 19.9 % / Biso Wilson estimate: 42.48 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.223 / Rpim(I) all: 0.051 / Rrim(I) all: 0.229 / Net I/σ(I): 8 / Num. measured all: 734925 / Scaling rejects: 791
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
2.06-2.1219.73.4345543728090.390.793.5251100
8.98-59.2116.70.0691385460.9990.0150.06221.799.9

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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: 2.06→57.07 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 1912 5.19 %
Rwork0.1893 34944 -
obs0.1913 36856 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.54 Å2 / Biso mean: 45.8096 Å2 / Biso min: 27.9 Å2
Refinement stepCycle: final / Resolution: 2.06→57.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 40 266 4266
Biso mean--60.51 48.85 -
Num. residues----524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.06-2.110.39711500.313824052555
2.11-2.170.34531310.297824322563
2.17-2.230.33871210.294624752596
2.23-2.30.29011480.281224472595
2.3-2.390.29211200.26724832603
2.39-2.480.33231160.252424652581
2.48-2.60.29561300.247424942624
2.6-2.730.27471310.230324922623
2.73-2.90.28361570.233224422599
2.9-3.130.27221400.211325052645
3.13-3.440.18221340.195525092643
3.44-3.940.21600.151825082668
3.94-4.960.15971420.138825582700
4.96-57.070.1981320.147627292861
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)
18.41813.0538-6.08374.6022-2.3115.9117-0.4088-0.5785-0.1613-0.73160.0404-0.06090.80480.23540.35510.59230.0044-0.08370.4366-0.01790.366616.8449-27.5862-16.715
23.64631.0207-0.07675.958-1.46295.4665-0.01660.4302-0.148-0.95660.18330.19920.0459-0.0485-0.12440.46180.0641-0.10260.45610.06480.388918.0147-7.722-23.3171
31.42570.37590.26852.13070.14882.74280.06850.04330.0908-0.06270.00320.0803-0.1123-0.0751-0.06840.31720.0057-0.00510.29750.03770.369121.1604-9.4978-6.4809
46.33312.02464.30093.8746-0.96948.2144-0.0391-0.0814-0.34540.06780.2414-0.09650.0371-0.1709-0.26950.4008-0.03090.00360.28180.00450.43322.1145-26.4295-1.9041
52.2755-0.72910.07046.34610.74483.13340.11620.0567-0.02470.4152-0.1176-0.48120.34790.2440.00680.31650.0162-0.05290.3827-0.02910.341651.7152-0.8975-20.6404
63.4799-0.47160.82372.5509-0.10342.3650.16340.07340.3585-0.1729-0.035-0.2453-0.2170.1207-0.12050.41440.00380.06080.29670.00770.353446.66427.7719-29.9586
71.8071-0.05760.1571.0440.23271.45630.19260.15280.0255-0.1216-0.0349-0.01430.01950.0449-0.15760.51690.0583-0.00440.34310.00840.356238.6934-3.403-35.729
87.65120.973-2.30472.02930.61744.3916-0.2128-0.0758-0.0360.0673-0.0609-0.20320.232-0.13190.30630.65170.06190.0060.32340.04460.368936.2006-14.4903-34.9733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 25 )A0 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 55 )A26 - 55
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 232 )A56 - 232
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 261 )A233 - 261
5X-RAY DIFFRACTION5chain 'B' and (resid 0 through 55 )B0 - 55
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 154 )B56 - 154
7X-RAY DIFFRACTION7chain 'B' and (resid 155 through 241 )B155 - 241
8X-RAY DIFFRACTION8chain 'B' and (resid 242 through 261 )B242 - 261

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