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- PDB-8h5o: Crystal structure of PETase S121E/P181V/D186H/N233C/S242T/N246D/S... -

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Basic information

Entry
Database: PDB / ID: 8h5o
TitleCrystal structure of PETase S121E/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
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: 2.1 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 1.1Oct 23, 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)31,5781
Polymers31,5781
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10000 Å2
Unit cell
Length a, b, c (Å)50.863, 52.620, 95.147
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 / PET hydrolase / PETase / PET-digesting enzyme


Mass: 31578.139 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20 % (W/V) PEG 3350, 0.2 M sodium fluoride

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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: Jun 26, 2022
RadiationProtocol: 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: 15455 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.047 / Rrim(I) all: 0.13 / Χ2: 6.117 / Net I/σ(I): 13.9 / Num. measured all: 121215
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.148.10.2847450.950.1070.3043.59100
2.14-2.188.10.2557700.9630.0960.2733.791100
2.18-2.2280.2317760.9680.0870.2474.076100
2.22-2.268.10.2347320.9750.0880.254.278100
2.26-2.318.10.2157620.9720.0810.2294.13100
2.31-2.3780.2037670.9720.0770.2174.261100
2.37-2.428.10.1967640.980.0740.214.571100
2.42-2.4980.197500.980.0710.2034.802100
2.49-2.5680.1857620.9860.070.1995.187100
2.56-2.6580.1657680.9840.0630.1775.506100
2.65-2.7480.1597590.9810.060.1715.84100
2.74-2.8580.1457800.9890.0550.1555.782100
2.85-2.987.90.1417580.9880.0540.1516.914100
2.98-3.147.90.1337790.9860.050.1427.601100
3.14-3.337.90.1227780.9880.0470.1318.024100
3.33-3.597.80.1077760.9920.0410.1148.156100
3.59-3.957.70.0987790.9940.0380.1059.06100
3.95-4.527.50.097910.9940.0350.0969.79498.8
4.52-5.77.40.0858110.9940.0330.0918.55799.8
5.7-506.50.0868480.9850.0360.0949.15897.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XJH

5xjh


Resolution: 2.1→29.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.299 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 756 4.9 %RANDOM
Rwork0.1406 ---
obs0.1429 14656 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.97 Å2 / Biso mean: 21.39 Å2 / Biso min: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0 Å2
2--2.17 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2.1→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 0 148 2074
Biso mean---35.87 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0111995
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161730
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.6342719
X-RAY DIFFRACTIONr_angle_other_deg0.511.5474048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.3051013
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78710296
X-RAY DIFFRACTIONr_chiral_restr0.0710.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02402
LS refinement shellResolution: 2.1→2.152 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.223 60 -
Rwork0.133 979 -
obs--92.77 %

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