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- PDB-7osb: Crystal Structure of a Double Mutant PETase (S238F/W159H) from Id... -

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Basic information

Entry
Database: PDB / ID: 7osb
TitleCrystal Structure of a Double Mutant PETase (S238F/W159H) from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE
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: 1.45 Å
AuthorsShakespeare, T.J. / Zahn, M. / Allen, M.D. / McGeehan, J.E.
Funding support United Kingdom, United States, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P011918/1 United Kingdom
Department of Energy (DOE, United States)DE-AC36-08GO28308 United States
CitationJournal: ChemSusChem / Year: 2022
Title: Comparative Performance of PETase as a Function of Reaction Conditions, Substrate Properties, and Product Accumulation.
Authors: Erickson, E. / Shakespeare, T.J. / Bratti, F. / Buss, B.L. / Graham, R. / Hawkins, M.A. / Konig, G. / Michener, W.E. / Miscall, J. / Ramirez, K.J. / Rorrer, N.A. / Zahn, M. / Pickford, A.R. ...Authors: Erickson, E. / Shakespeare, T.J. / Bratti, F. / Buss, B.L. / Graham, R. / Hawkins, M.A. / Konig, G. / Michener, W.E. / Miscall, J. / Ramirez, K.J. / Rorrer, N.A. / Zahn, M. / Pickford, A.R. / McGeehan, J.E. / Beckham, G.T.
History
DepositionJun 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
B: Poly(ethylene terephthalate) hydrolase
C: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,31318
Polymers94,0623
Non-polymers1,25115
Water19,4921082
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6785
Polymers31,3541
Non-polymers3244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9628
Polymers31,3541
Non-polymers6087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6745
Polymers31,3541
Non-polymers3204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.379, 233.957, 164.808
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-613-

HOH

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 31353.955 Da / Num. of mol.: 3 / Mutation: S238F, W159H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1082 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.95M Ammonium Sulfate, 0.1M Sodium Citrate, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→20.7 Å / Num. obs: 178688 / % possible obs: 99.69 % / Redundancy: 1.99 % / Biso Wilson estimate: 18.11 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02805 / Rpim(I) all: 0.02805 / Rrim(I) all: 0.03966 / Net I/σ(I): 9.99
Reflection shellResolution: 1.45→1.502 Å / Rmerge(I) obs: 0.6994 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 17558 / CC1/2: 0.639 / CC star: 0.883 / Rpim(I) all: 0.6994 / Rrim(I) all: 0.9891 / % possible all: 98.83

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
MOLREPphasing
xia2data processing
DIALSdata reduction
xia2data reduction
DIALSdata reduction
xia2data scaling
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EQE

6eqe


Resolution: 1.45→21.02 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.06 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.064 / SU Rfree Cruickshank DPI: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 8759 -RANDOM
Rwork0.1909 ---
obs0.1917 178676 99.9 %-
Displacement parametersBiso mean: 30.28 Å2
Baniso -1Baniso -2Baniso -3
1--15.8946 Å20 Å20 Å2
2--10.9959 Å20 Å2
3---4.8988 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.45→21.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 65 1082 6995
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086102HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.948327HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1996SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1055HARMONIC5
X-RAY DIFFRACTIONt_it6102HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion828SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6709SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.16
X-RAY DIFFRACTIONt_other_torsion12.96
LS refinement shellResolution: 1.45→1.46 Å
RfactorNum. reflection% reflection
Rfree0.3728 170 -
Rwork0.3874 --
obs0.3867 3574 95.71 %
Refinement TLS params.

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)
10.0975-0.1397-0.32650.79480.26360.5650.1065-0.0281-0.0735-0.02810.00990.027-0.07350.027-0.1164-0.06140.02920.00030.0319-0.01610.01984.1964-59.0433-13.1823
20.1119-0.2475-0.12720.78290.05460.3054-0.0627-0.01870.1361-0.01870.0088-0.00540.1361-0.00540.05390.11630.0412-0.0116-0.0537-0.0118-0.05915.4361-99.7667-21.8643
30.0449-0.04410.13490.4827-0.27350.5802-0.00270.0724-0.12850.0724-0.04980.0011-0.12850.00110.05260.08550.05480.0445-0.03660.0307-0.03725.3645-136.342-23.5881
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A28 - 293
2X-RAY DIFFRACTION1{ A|* }A301
3X-RAY DIFFRACTION2{ B|* }B28 - 291
4X-RAY DIFFRACTION2{ B|* }B307 - 313
5X-RAY DIFFRACTION3{ C|* }C28 - 291
6X-RAY DIFFRACTION3{ C|* }C305 - 307

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