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- PDB-6kuq: Crystal strcuture of PETase A248D, R280K mutant from Ideonella sa... -

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Basic information

Entry
Database: PDB / ID: 6kuq
TitleCrystal strcuture of PETase A248D, R280K mutant from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / PET hydrolase
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
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsJoo, S. / Kim, K.-J.
CitationJournal: To Be Published
Title: Crystal strcuture of PETase A248D, R280K mutant from Ideonella sakaiensis
Authors: Joo, S. / Kim, K.-J.
History
DepositionSep 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase


Theoretical massNumber of molelcules
Total (without water)31,5071
Polymers31,5071
Non-polymers00
Water2,522140
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 area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.236, 51.236, 179.091
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PETase / PET-digesting enzyme


Mass: 31506.908 Da / Num. of mol.: 1 / Mutation: A248D, R280K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6) (bacteria)
Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 17% PEG 10K, 0.1M Bis-Tris, pH 5.0, 0.15M Ammonium acetate

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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: 0.97834 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97834 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 21740 / % possible obs: 98.1 % / Redundancy: 9.6 % / Rrim(I) all: 0.148 / Net I/σ(I): 55.22
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 1025 / Rrim(I) all: 0.332

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5xjh

5xjh


Resolution: 1.91→27.89 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.237 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.119
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 1078 5 %RANDOM
Rwork0.1557 ---
obs0.1574 20619 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.34 Å2 / Biso mean: 9.899 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.16 Å2-0 Å2
2---0.33 Å20 Å2
3---1.06 Å2
Refinement stepCycle: final / Resolution: 1.91→27.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 0 140 2080
Biso mean---17.37 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171745
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.6392703
X-RAY DIFFRACTIONr_angle_other_deg1.5331.5684066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.8922290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41315296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0641512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
LS refinement shellResolution: 1.91→1.957 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.187 91 -
Rwork0.164 1347 -
obs--89.54 %

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