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- PDB-6jtu: Crystal structure of MHETase from Ideonella sakaiensis -

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Basic information

Entry
Database: PDB / ID: 6jtu
TitleCrystal structure of MHETase from Ideonella sakaiensis
ComponentsMono(2-hydroxyethyl) terephthalate hydrolase
KeywordsHYDROLASE
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
ACETATE ION / FORMIC ACID / Mono(2-hydroxyethyl) terephthalate hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsSagong, H.-Y. / Seo, H. / Kim, K.-J.
CitationJournal: Acs Catalysis / Year: 2020
Title: Decomposition of PET film by MHETase using Exo-PETase function
Authors: Sagong, H.-Y. / Seo, H. / Kim, T. / Son, H. / Joo, S. / Lee, S. / Kim, S. / Woo, J.-S. / Hwang, S. / Kim, K.-J.
History
DepositionApr 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: Mono(2-hydroxyethyl) terephthalate hydrolase
C: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,92222
Polymers192,5343
Non-polymers1,38819
Water12,935718
1
A: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5397
Polymers64,1781
Non-polymers3616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8309
Polymers64,1781
Non-polymers6528
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Mono(2-hydroxyethyl) terephthalate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5536
Polymers64,1781
Non-polymers3755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.931, 173.163, 107.225
Angle α, β, γ (deg.)90.000, 119.860, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 64178.004 Da / Num. of mol.: 3 / Fragment: feruloyl esterase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: 201-F6 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0K8P8E7, mono(ethylene terephthalate) hydrolase

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Non-polymers , 6 types, 737 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.49 Å3/Da / Density % sol: 72.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, HEPES, Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2018
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 196929 / % possible obs: 97.7 % / Redundancy: 3.5 % / CC1/2: 0.977 / Rpim(I) all: 0.063 / Net I/σ(I): 22.9
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 9385 / CC1/2: 0.861 / Rpim(I) all: 0.175

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→33.21 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.393 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 9652 5 %RANDOM
Rwork0.1705 ---
obs0.1719 182668 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.53 Å2 / Biso mean: 29.49 Å2 / Biso min: 19.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å2-0 Å2-0.33 Å2
2---3.2 Å2-0 Å2
3---3.25 Å2
Refinement stepCycle: final / Resolution: 2.1→33.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12420 0 86 718 13224
Biso mean--45.77 32.94 -
Num. residues----1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01312825
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711342
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.63717447
X-RAY DIFFRACTIONr_angle_other_deg1.4771.57226252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96951680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.91121.762630
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.334151779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9121584
X-RAY DIFFRACTIONr_chiral_restr0.080.21641
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022842
LS refinement shellResolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 655 -
Rwork0.245 13263 -
all-13918 -
obs--95.51 %

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