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- PDB-8h5j: Crystal structure of PETase S121E/A180V/P181V/D186H/N233C/S242T/N... -

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Basic information

Entry
Database: PDB / ID: 8h5j
TitleCrystal structure of PETase S121E/A180V/P181V/D186H/N233C/S242T/N246D/S282C mutant from Ideonella sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / Ideonella sakaiensis / mutant
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 / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / PHOSPHATE ION / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLee, S.H. / Seo, H. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: A case of balance engineering exhibits kinetic relationship between mesophilic and thermophilic poly(ethylene terephthalate) depolymerases.
Authors: Lee, S.H. / Seo, H. / Kim, K.J.
History
DepositionOct 13, 2022Deposition site: PDBJ / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7079
Polymers63,2122
Non-polymers4947
Water9,422523
1
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8354
Polymers31,6061
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8715
Polymers31,6061
Non-polymers2654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.218, 50.665, 80.854
Angle α, β, γ (deg.)90.000, 124.640, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-626-

HOH

21B-760-

HOH

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Components

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


Mass: 31606.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.86 Å3/Da / Density % sol: 33.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25 % PEG3350, 0.1 M BIS-TRIS pH6.5, and 0.2 M Ammonium sulfate

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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: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→28.65 Å / Num. obs: 88810 / % possible obs: 98.3 % / Redundancy: 1.6 % / CC1/2: 0.984 / Net I/σ(I): 30
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 4312 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0350refinement
PDB_EXTRACT3.27data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 1.4→28.65 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.148 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19 4424 5 %RANDOM
Rwork0.1565 ---
obs0.1581 84386 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.44 Å2 / Biso mean: 17.278 Å2 / Biso min: 9.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å20.27 Å2
2---0.03 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 1.4→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 24 523 4403
Biso mean--32.76 33.33 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0114276
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163679
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.6355858
X-RAY DIFFRACTIONr_angle_other_deg0.6121.5488633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.2671034
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86810651
X-RAY DIFFRACTIONr_chiral_restr0.0950.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02884
LS refinement shellResolution: 1.404→1.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 292 -
Rwork0.273 5928 -
all-6220 -
obs--93.23 %

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