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

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Basic information

Entry
Database: PDB / ID: 6eqf
TitleCrystal structure of a polyethylene terephthalate degrading hydrolase from Ideonella sakaiensis in spacegroup P212121
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: 1.7 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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3772
Polymers31,3421
Non-polymers351
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.349, 64.130, 68.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31341.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli) / Strain (production host): C41
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 1.81 Å3/Da / Density % sol: 32.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 NH4Cl, 0.1 M MES, pH 6.0 20% PEG 6000

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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: 1.7→68.24 Å / Num. obs: 25470 / % possible obs: 98.8 % / Redundancy: 5.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.049 / Rrim(I) all: 0.118 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3652 / CC1/2: 0.905 / Rpim(I) all: 0.147 / Rrim(I) all: 0.356 / % possible all: 100

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Processing

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

6eqd


Resolution: 1.7→46.732 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 1269 4.99 %
Rwork0.1487 --
obs0.1505 25409 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→46.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 1 325 2318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072077
X-RAY DIFFRACTIONf_angle_d0.8472841
X-RAY DIFFRACTIONf_dihedral_angle_d2.3662086
X-RAY DIFFRACTIONf_chiral_restr0.058311
X-RAY DIFFRACTIONf_plane_restr0.006377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76810.23061340.16952629X-RAY DIFFRACTION100
1.7681-1.84850.21951550.15822614X-RAY DIFFRACTION100
1.8485-1.9460.221400.15232668X-RAY DIFFRACTION100
1.946-2.06790.17661320.1492657X-RAY DIFFRACTION100
2.0679-2.22760.18061240.14372672X-RAY DIFFRACTION100
2.2276-2.45170.18731400.14222666X-RAY DIFFRACTION100
2.4517-2.80650.17711530.14792676X-RAY DIFFRACTION100
2.8065-3.53570.18731380.14672715X-RAY DIFFRACTION100
3.5357-46.74960.16981530.14862843X-RAY DIFFRACTION100

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