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- PDB-6ij3: Crystal structure of PETase S121D, D186H mutant from Ideonella sa... -

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Basic information

Entry
Database: PDB / ID: 6ij3
TitleCrystal structure of PETase S121D, D186H 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: 1.4 Å
AuthorsJoo, S. / Kim, K.J.
CitationJournal: Acs Catalysis / Year: 2019
Title: Rational Protein Engineering of Thermo-Stable PETase from Ideonella sakaiensis for Highly Efficient PET Degradation
Authors: Son, H.F. / Cho, I.J. / Joo, S. / Seo, H. / Sagong, H.Y. / Choi, S.Y. / Lee, S.Y. / Kim, K.J.
History
DepositionOct 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
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)31,5701
Polymers31,5701
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9760 Å2
Unit cell
Length a, b, c (Å)115.427, 50.631, 41.491
Angle α, β, γ (deg.)90.00, 93.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 31570.064 Da / Num. of mol.: 1 / Mutation: S121D, D186H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / 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.: 225 / 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: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Tris, PEG 3000, NaCl

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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: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 46596 / % possible obs: 99 % / Redundancy: 3.2 % / Rpim(I) all: 0.067 / Net I/σ(I): 25.99
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 2301 / Rpim(I) all: 0.215

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.4→21.61 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.399 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23322 2311 5 %RANDOM
Rwork0.19443 ---
obs0.19633 44285 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.447 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-0.92 Å2
2--0.03 Å2-0 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.4→21.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 0 225 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131966
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171729
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.6392677
X-RAY DIFFRACTIONr_angle_other_deg1.5441.5674022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2125260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.10621.44490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83315289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0211513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7141.5991043
X-RAY DIFFRACTIONr_mcbond_other1.7121.5981042
X-RAY DIFFRACTIONr_mcangle_it2.3982.3981302
X-RAY DIFFRACTIONr_mcangle_other2.3982.3991303
X-RAY DIFFRACTIONr_scbond_it2.2171.808923
X-RAY DIFFRACTIONr_scbond_other2.2161.809924
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3372.6291376
X-RAY DIFFRACTIONr_long_range_B_refined4.6820.3722263
X-RAY DIFFRACTIONr_long_range_B_other4.620.0742236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 162 -
Rwork0.275 3191 -
obs--97.33 %

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