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- PDB-5yns: Crystal structure of PETase R280A mutant from Ideonella sakaiensis -

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Basic information

Entry
Database: PDB / ID: 5yns
TitleCrystal structure of PETase R280A mutant from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE
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 family / Cutinase / PET hydrolase-like / : / 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: 1.36 Å
AuthorsJoo, S. / Kim, K.-J.
CitationJournal: Nat Commun / Year: 2018
Title: Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation.
Authors: Joo, S. / Cho, I.J. / Seo, H. / Son, H.F. / Sagong, H.-Y. / Shin, T.J. / Choi, S.Y. / Lee, S.Y. / Kim, K.-J.
History
DepositionOct 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 22, 2023Group: 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 1.3Oct 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: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)27,5911
Polymers27,5911
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.607, 50.586, 129.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PETase


Mass: 27590.596 Da / Num. of mol.: 1 / Fragment: a/b hydrolase superfamily / Mutation: R280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria)
Strain: 201-F6 / Gene: ISF6_4831 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami-b
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: BIS-Tris, Ammonium acetate, PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 62494 / % possible obs: 98.7 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 40.79
Reflection shellRmerge(I) obs: 0.374

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.36→27.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.858 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.052
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1904 3116 5.1 %RANDOM
Rwork0.1612 ---
obs0.1627 58473 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.25 Å2 / Biso mean: 14.344 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å2-0 Å2
2---0.45 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.36→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 0 294 2227
Biso mean---29.46 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192009
X-RAY DIFFRACTIONr_bond_other_d0.0010.021825
X-RAY DIFFRACTIONr_angle_refined_deg2.2491.9322740
X-RAY DIFFRACTIONr_angle_other_deg1.0373.0024198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27523.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32315296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5651513
X-RAY DIFFRACTIONr_chiral_restr0.1510.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
LS refinement shellResolution: 1.36→1.396 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 236 -
Rwork0.274 4047 -
all-4283 -
obs--94.61 %

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