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

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Basic information

Entry
Database: PDB / ID: 6eqg
TitleCrystal structure of a polyethylene terephthalate degrading hydrolase from Ideonella sakaiensis in spacegroup P21
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / PET degradation / a/b hydrolase
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / carboxylic ester hydrolase activity / cellular response to organic substance / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / 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: 1.799 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)94,1936
Polymers94,0263
Non-polymers1673
Water20,7711153
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3772
Polymers31,3421
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4733
Polymers31,3421
Non-polymers1322
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)69.149, 46.381, 119.581
Angle α, β, γ (deg.)90.00, 93.19, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 1153 / Source method: isolated from a natural source / Formula: H2O

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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: 2.05 Å3/Da / Density % sol: 40.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M LiSO4, 0.1 M Bis-Tris, pH 5.5 25% PEG3350

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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: 1.8→46.46 Å / Num. obs: 68988 / % possible obs: 97.7 % / Redundancy: 3.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.065 / Rrim(I) all: 0.121 / Net I/σ(I): 8.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 9836 / CC1/2: 0.766 / Rpim(I) all: 0.342 / Rrim(I) all: 0.639 / % possible all: 95.9

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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: 1.799→46.456 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1838 3550 5.15 %
Rwork0.1514 --
obs0.153 68954 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→46.456 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5783 0 7 1153 6943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035950
X-RAY DIFFRACTIONf_angle_d0.5988119
X-RAY DIFFRACTIONf_dihedral_angle_d2.4834376
X-RAY DIFFRACTIONf_chiral_restr0.045896
X-RAY DIFFRACTIONf_plane_restr0.0041071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7994-1.82410.28671440.24512462X-RAY DIFFRACTION93
1.8241-1.85010.2611540.21772579X-RAY DIFFRACTION97
1.8501-1.87770.22481460.2012540X-RAY DIFFRACTION97
1.8777-1.90710.23111480.19972551X-RAY DIFFRACTION96
1.9071-1.93830.211330.18242615X-RAY DIFFRACTION97
1.9383-1.97180.23621540.1742565X-RAY DIFFRACTION97
1.9718-2.00760.19381340.16962586X-RAY DIFFRACTION97
2.0076-2.04620.21541240.1732627X-RAY DIFFRACTION97
2.0462-2.0880.21031350.1672609X-RAY DIFFRACTION97
2.088-2.13340.2251400.15772590X-RAY DIFFRACTION97
2.1334-2.1830.23051370.15412605X-RAY DIFFRACTION97
2.183-2.23760.19361480.14972578X-RAY DIFFRACTION98
2.2376-2.29810.19711320.1512640X-RAY DIFFRACTION98
2.2981-2.36570.18611510.15152585X-RAY DIFFRACTION98
2.3657-2.44210.1941550.15932638X-RAY DIFFRACTION98
2.4421-2.52940.21591480.15452581X-RAY DIFFRACTION98
2.5294-2.63060.14981430.1482621X-RAY DIFFRACTION98
2.6306-2.75040.20051170.15022683X-RAY DIFFRACTION98
2.7504-2.89530.18241450.14522638X-RAY DIFFRACTION98
2.8953-3.07670.1951640.14362623X-RAY DIFFRACTION98
3.0767-3.31420.18341340.13992698X-RAY DIFFRACTION99
3.3142-3.64760.14741450.13192635X-RAY DIFFRACTION98
3.6476-4.17510.13341340.11952688X-RAY DIFFRACTION98
4.1751-5.25910.13541330.12542708X-RAY DIFFRACTION99
5.2591-46.47190.16261520.16392759X-RAY DIFFRACTION98

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