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- PDB-6eqe: High resolution crystal structure of a polyethylene terephthalate... -

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Basic information

Entry
Database: PDB / ID: 6eqe
TitleHigh resolution crystal structure of a polyethylene terephthalate degrading hydrolase from Ideonella sakaiensis
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 / 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: 0.92 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4595
Polymers31,3421
Non-polymers1174
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-35 kcal/mol
Surface area10280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.114, 51.388, 84.545
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 (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


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 1.79 Å3/Da / Density % sol: 31.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.2 M MgCl2, 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: I23 / Wavelength: 1.2398 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 0.92→84.54 Å / Num. obs: 154417 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.018 / Rrim(I) all: 0.048 / Net I/σ(I): 17.4
Reflection shellResolution: 0.92→0.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 22309 / CC1/2: 0.852 / Rpim(I) all: 0.254 / Rrim(I) all: 0.254 / % possible all: 99.8

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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: 0.92→27.513 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 9.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1101 8053 5.22 %
Rwork0.1001 --
obs0.1006 154294 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.92→27.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 4 393 2349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072174
X-RAY DIFFRACTIONf_angle_d1.1042997
X-RAY DIFFRACTIONf_dihedral_angle_d12.676837
X-RAY DIFFRACTIONf_chiral_restr0.093332
X-RAY DIFFRACTIONf_plane_restr0.01396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.92-0.93050.23373010.21524760X-RAY DIFFRACTION99
0.9305-0.94140.22422310.19694848X-RAY DIFFRACTION100
0.9414-0.95290.21592660.19724830X-RAY DIFFRACTION100
0.9529-0.9650.20622690.18564801X-RAY DIFFRACTION100
0.965-0.97770.20782470.18664831X-RAY DIFFRACTION99
0.9777-0.9910.18782840.1784778X-RAY DIFFRACTION99
0.991-1.00520.16812720.15034853X-RAY DIFFRACTION100
1.0052-1.02020.12822490.13164832X-RAY DIFFRACTION100
1.0202-1.03620.13272690.12134836X-RAY DIFFRACTION100
1.0362-1.05310.12312940.11594814X-RAY DIFFRACTION100
1.0531-1.07130.11462650.10174851X-RAY DIFFRACTION100
1.0713-1.09080.11472770.09874798X-RAY DIFFRACTION100
1.0908-1.11180.10872520.09284886X-RAY DIFFRACTION100
1.1118-1.13450.09162290.08294876X-RAY DIFFRACTION100
1.1345-1.15910.09482590.08224852X-RAY DIFFRACTION100
1.1591-1.18610.09472390.08124879X-RAY DIFFRACTION100
1.1861-1.21580.09482530.07734860X-RAY DIFFRACTION100
1.2158-1.24860.08182460.07344901X-RAY DIFFRACTION100
1.2486-1.28540.08213090.07494830X-RAY DIFFRACTION100
1.2854-1.32680.08683040.07484819X-RAY DIFFRACTION100
1.3268-1.37430.08532660.07664883X-RAY DIFFRACTION100
1.3743-1.42930.08682680.07714892X-RAY DIFFRACTION100
1.4293-1.49430.09262660.07324890X-RAY DIFFRACTION100
1.4943-1.57310.08912850.07454879X-RAY DIFFRACTION100
1.5731-1.67170.09263020.07524857X-RAY DIFFRACTION100
1.6717-1.80070.09162880.08224928X-RAY DIFFRACTION100
1.8007-1.98190.09912830.08454936X-RAY DIFFRACTION100
1.9819-2.26850.08962460.094980X-RAY DIFFRACTION100
2.2685-2.85770.11442600.10155045X-RAY DIFFRACTION100
2.8577-27.52540.13072740.12795216X-RAY DIFFRACTION100

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