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- PDB-6eqh: Crystal structure of a polyethylene terephthalate degrading hydro... -

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Basic information

Entry
Database: PDB / ID: 6eqh
TitleCrystal structure of a polyethylene terephthalate degrading hydrolase from Ideonella sakaiensis in spacegroup C2221
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / PET degradation / a/b hydrolase
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase family / Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsAustin, H.P. / Allen, M.D. / Johnson, C.W. / Beckham, G.T. / McGeehan, J.E.
Funding support United States, United Kingdom, 2items
OrganizationGrant numberCountry
NRELLaboratory Directed Research and Development Program United States
Biotechnology and Biological Sciences Research CouncilBB/P011918/1 United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Characterization and engineering of a plastic-degrading aromatic polyesterase.
Authors: Austin, H.P. / Allen, M.D. / Donohoe, B.S. / Rorrer, N.A. / Kearns, F.L. / Silveira, R.L. / Pollard, B.C. / Dominick, G. / Duman, R. / El Omari, K. / Mykhaylyk, V. / Wagner, A. / Michener, W. ...Authors: Austin, H.P. / Allen, M.D. / Donohoe, B.S. / Rorrer, N.A. / Kearns, F.L. / Silveira, R.L. / Pollard, B.C. / Dominick, G. / Duman, R. / El Omari, K. / Mykhaylyk, V. / Wagner, A. / Michener, W.E. / Amore, A. / Skaf, M.S. / Crowley, M.F. / Thorne, A.W. / Johnson, C.W. / Woodcock, H.L. / McGeehan, J.E. / Beckham, G.T.
History
DepositionOct 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)94,0263
Polymers94,0263
Non-polymers00
Water17,835990
1
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)31,3421
Polymers31,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)31,3421
Polymers31,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)31,3421
Polymers31,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.702, 234.134, 165.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21A-519-

HOH

31C-581-

HOH

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PETase


Mass: 31341.924 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria)
Gene: ISF6_4831 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6M MgSO4, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.58→49.81 Å / Num. obs: 139895 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.021 / Rrim(I) all: 0.053 / Net I/σ(I): 18.2
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 20255 / CC1/2: 0.886 / Rpim(I) all: 0.314 / Rrim(I) all: 0.807 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EQD

6eqd


Resolution: 1.58→43.676 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1841 6926 4.96 %
Rwork0.1691 --
obs0.1699 139743 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→43.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 0 990 6790
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075995
X-RAY DIFFRACTIONf_angle_d0.8268186
X-RAY DIFFRACTIONf_dihedral_angle_d2.6074831
X-RAY DIFFRACTIONf_chiral_restr0.055904
X-RAY DIFFRACTIONf_plane_restr0.0061081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.5980.34552460.34574386X-RAY DIFFRACTION99
1.598-1.61680.32752570.30524304X-RAY DIFFRACTION100
1.6168-1.63650.34252220.29564404X-RAY DIFFRACTION100
1.6365-1.65720.29222500.27564357X-RAY DIFFRACTION100
1.6572-1.6790.27962330.25754378X-RAY DIFFRACTION100
1.679-1.7020.26872560.24864385X-RAY DIFFRACTION100
1.702-1.72630.26242170.23284360X-RAY DIFFRACTION100
1.7263-1.75210.24092300.22844421X-RAY DIFFRACTION100
1.7521-1.77950.23942230.20864358X-RAY DIFFRACTION100
1.7795-1.80860.25192320.1994420X-RAY DIFFRACTION100
1.8086-1.83980.20972130.20194389X-RAY DIFFRACTION100
1.8398-1.87330.23882130.19244436X-RAY DIFFRACTION100
1.8733-1.90930.24032150.19834391X-RAY DIFFRACTION100
1.9093-1.94830.20562210.19454415X-RAY DIFFRACTION100
1.9483-1.99060.20812130.17764412X-RAY DIFFRACTION100
1.9906-2.0370.18522140.17094434X-RAY DIFFRACTION100
2.037-2.08790.18112270.17484409X-RAY DIFFRACTION100
2.0879-2.14430.21732250.17474410X-RAY DIFFRACTION100
2.1443-2.20740.18932390.16954430X-RAY DIFFRACTION100
2.2074-2.27870.18062350.16744424X-RAY DIFFRACTION100
2.2787-2.36010.16932220.16254423X-RAY DIFFRACTION100
2.3601-2.45460.17712240.16854430X-RAY DIFFRACTION100
2.4546-2.56630.17672450.16784426X-RAY DIFFRACTION100
2.5663-2.70160.19222240.16484456X-RAY DIFFRACTION100
2.7016-2.87080.1812360.1674443X-RAY DIFFRACTION100
2.8708-3.09240.17572190.16164515X-RAY DIFFRACTION100
3.0924-3.40350.16822070.15554476X-RAY DIFFRACTION100
3.4035-3.89580.13682610.14094488X-RAY DIFFRACTION100
3.8958-4.90720.15682440.13054529X-RAY DIFFRACTION100
4.9072-43.6930.17792630.16764708X-RAY DIFFRACTION99

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