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- PDB-6qz1: Structure of MHETase from Ideonella sakaiensis -

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Basic information

Entry
Database: PDB / ID: 6qz1
TitleStructure of MHETase from Ideonella sakaiensis
ComponentsMono(2-hydroxyethyl) terephthalate hydrolase
KeywordsHYDROLASE / plastic-binding protein / MHETase / PET degradation / STRUCTURAL GENOMICS
Function / homology
Function and homology information


mono(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / cell outer membrane / metal ion binding
Similarity search - Function
Tannase/feruloyl esterase / Tannase and feruloyl esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
BENZOIC ACID / Mono(2-hydroxyethyl) terephthalate hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAllen, M.D. / Johnson, C.W. / Knott, B.C. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P011918/1 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Characterization and engineering of a two-enzyme system for plastics depolymerization.
Authors: Knott, B.C. / Erickson, E. / Allen, M.D. / Gado, J.E. / Graham, R. / Kearns, F.L. / Pardo, I. / Topuzlu, E. / Anderson, J.J. / Austin, H.P. / Dominick, G. / Johnson, C.W. / Rorrer, N.A. / ...Authors: Knott, B.C. / Erickson, E. / Allen, M.D. / Gado, J.E. / Graham, R. / Kearns, F.L. / Pardo, I. / Topuzlu, E. / Anderson, J.J. / Austin, H.P. / Dominick, G. / Johnson, C.W. / Rorrer, N.A. / Szostkiewicz, C.J. / Copie, V. / Payne, C.M. / Woodcock, H.L. / Donohoe, B.S. / Beckham, G.T. / McGeehan, J.E.
History
DepositionMar 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 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: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3993
Polymers59,2371
Non-polymers1622
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint5 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.195, 89.875, 91.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-875-

HOH

21A-1324-

HOH

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Components

#1: Protein Mono(2-hydroxyethyl) terephthalate hydrolase / MHETase


Mass: 59237.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria)
Gene: ISF6_0224 / Plasmid: pCJ136 / Production host: Escherichia coli (E. coli) / Variant (production host): C41
References: UniProt: A0A0K8P8E7, mono(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M sodium acetate (pH 5.5), 24% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→46 Å / Num. obs: 70855 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 15.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 10080 / CC1/2: 0.9 / Rrim(I) all: 0.634 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QZ3

6qz3


Resolution: 1.7→45.998 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.62 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.1918 6747 5 %
Rwork0.1645 --
obs0.1659 70749 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→45.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 10 552 4691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084269
X-RAY DIFFRACTIONf_angle_d0.95820
X-RAY DIFFRACTIONf_dihedral_angle_d3.9563368
X-RAY DIFFRACTIONf_chiral_restr0.055610
X-RAY DIFFRACTIONf_plane_restr0.006778
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.25751860.26624088X-RAY DIFFRACTION94
1.7193-1.73950.29762250.2494301X-RAY DIFFRACTION100
1.7395-1.76080.2652350.23084288X-RAY DIFFRACTION100
1.7608-1.78310.22382320.22934252X-RAY DIFFRACTION100
1.7831-1.80650.26392770.22744280X-RAY DIFFRACTION100
1.8065-1.83130.26432100.22264336X-RAY DIFFRACTION100
1.8313-1.85740.3022720.24254228X-RAY DIFFRACTION100
1.8574-1.88520.2752440.23644323X-RAY DIFFRACTION100
1.8852-1.91460.24842170.23054313X-RAY DIFFRACTION100
1.9146-1.9460.27142060.21864292X-RAY DIFFRACTION100
1.946-1.97960.2462240.20514275X-RAY DIFFRACTION100
1.9796-2.01560.27462570.19544244X-RAY DIFFRACTION100
2.0156-2.05430.21832110.19294338X-RAY DIFFRACTION100
2.0543-2.09630.22772060.19314296X-RAY DIFFRACTION100
2.0963-2.14180.21432440.18414353X-RAY DIFFRACTION100
2.1418-2.19170.23322100.18264276X-RAY DIFFRACTION100
2.1917-2.24650.21872220.1854268X-RAY DIFFRACTION99
2.2465-2.30720.21652310.17974275X-RAY DIFFRACTION99
2.3072-2.37510.20312380.17654274X-RAY DIFFRACTION100
2.3751-2.45170.20771840.17494298X-RAY DIFFRACTION100
2.4517-2.53940.21232580.17714264X-RAY DIFFRACTION100
2.5394-2.6410.21312220.17254313X-RAY DIFFRACTION99
2.641-2.76120.1761860.17134301X-RAY DIFFRACTION99
2.7612-2.90680.18512330.16584226X-RAY DIFFRACTION99
2.9068-3.08890.20612460.16054231X-RAY DIFFRACTION98
3.0889-3.32730.18311740.16454287X-RAY DIFFRACTION98
3.3273-3.6620.17872490.15214179X-RAY DIFFRACTION98
3.662-4.19160.17131710.13554261X-RAY DIFFRACTION98
4.1916-5.27970.13712550.1194189X-RAY DIFFRACTION98
5.2797-45.9980.14272220.14394227X-RAY DIFFRACTION98

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