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- PDB-6qz4: Structure of MHETase from Ideonella sakaiensis -

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Basic information

Entry
Database: PDB / ID: 6qz4
TitleStructure of MHETase from Ideonella sakaiensis
ComponentsMono(2-hydroxyethyl) terephthalate hydrolase
KeywordsHYDROLASE / MHETase / PET degradation / STRUCTURAL GENOMICS / plastic-binding protein
Function / homologymono(ethylene terephthalate) hydrolase / Tannase/feruloyl esterase / Tannase and feruloyl esterase / carboxylic ester hydrolase activity / xenobiotic catabolic process / cell outer membrane / Alpha/Beta hydrolase fold / metal ion binding / Mono(2-hydroxyethyl) terephthalate hydrolase
Function and homology information
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 CouncilBB/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 11, 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mono(2-hydroxyethyl) terephthalate hydrolase
B: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7166
Polymers128,4432
Non-polymers2724
Water25,3471407
1
A: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3583
Polymers64,2221
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,3583
Polymers64,2221
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.212, 92.804, 159.991
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 Mono(2-hydroxyethyl) terephthalate hydrolase / MHETase


Mass: 64221.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1407 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: ammonium acetate (pH 4.5), 22.5% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→46.24 Å / Num. obs: 122377 / % possible obs: 98.2 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 14.7
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 17402 / CC1/2: 0.914 / Rpim(I) all: 0.231 / Rrim(I) all: 0.598 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QZ1

6qz1


Resolution: 1.8→46.239 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.2051 11726 4.99 %
Rwork0.1824 --
obs0.1836 122208 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→46.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 12 1407 9805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038679
X-RAY DIFFRACTIONf_angle_d0.60711851
X-RAY DIFFRACTIONf_dihedral_angle_d3.7826873
X-RAY DIFFRACTIONf_chiral_restr0.0421242
X-RAY DIFFRACTIONf_plane_restr0.0041591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.2843870.27347152X-RAY DIFFRACTION94
1.8205-1.84190.26623550.25597439X-RAY DIFFRACTION98
1.8419-1.86440.28574230.24517287X-RAY DIFFRACTION97
1.8644-1.8880.26323590.24157500X-RAY DIFFRACTION97
1.888-1.91280.25593640.23867430X-RAY DIFFRACTION97
1.9128-1.9390.25323920.23557348X-RAY DIFFRACTION97
1.939-1.96670.24984140.22447433X-RAY DIFFRACTION98
1.9667-1.99610.26343740.22117469X-RAY DIFFRACTION98
1.9961-2.02730.25363740.21747447X-RAY DIFFRACTION97
2.0273-2.06050.24134450.21497354X-RAY DIFFRACTION97
2.0605-2.0960.25644100.20467358X-RAY DIFFRACTION98
2.096-2.13420.2354140.20387440X-RAY DIFFRACTION98
2.1342-2.17520.25413480.27478X-RAY DIFFRACTION98
2.1752-2.21960.23063430.19387538X-RAY DIFFRACTION98
2.2196-2.26790.22093790.19537536X-RAY DIFFRACTION98
2.2679-2.32060.21463240.19427446X-RAY DIFFRACTION98
2.3206-2.37860.25434140.19467427X-RAY DIFFRACTION98
2.3786-2.4430.21433420.1887537X-RAY DIFFRACTION98
2.443-2.51480.21734430.18797462X-RAY DIFFRACTION99
2.5148-2.5960.19473740.18287489X-RAY DIFFRACTION98
2.596-2.68880.22373950.19057477X-RAY DIFFRACTION99
2.6888-2.79640.20394320.18297452X-RAY DIFFRACTION98
2.7964-2.92370.18534710.18747445X-RAY DIFFRACTION99
2.9237-3.07780.20744300.17517529X-RAY DIFFRACTION99
3.0778-3.27060.20624020.17827498X-RAY DIFFRACTION99
3.2706-3.5230.18453460.17217536X-RAY DIFFRACTION98
3.523-3.87740.18344660.16437433X-RAY DIFFRACTION98
3.8774-4.43810.16713320.14877576X-RAY DIFFRACTION99
4.4381-5.590.1753880.14797575X-RAY DIFFRACTION99
5.59-46.25450.15633860.16357395X-RAY DIFFRACTION97

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