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- PDB-8cmv: Engineered PETase enzyme from LCC - C09 mutant -

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Basic information

Entry
Database: PDB / ID: 8cmv
TitleEngineered PETase enzyme from LCC - C09 mutant
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / Plastic degradation / Thermal stablization / MHET / BHET / TPA
Function / homology
Function and homology information


poly(ethylene terephthalate) hydrolase / acetylesterase activity / cutinase activity / cutinase / extracellular region
Similarity search - Function
Alpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesunidentified prokaryotic organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsBhattacharya, S. / Estiri, H. / Castagna, R. / Parisini, E.
Funding support Latvia, 1items
OrganizationGrant numberCountry
Other governmentlzp-2020/2-0013 Latvia
CitationJournal: To Be Published
Title: Engineered PETase Enzyme
Authors: Bhattacharya, S. / Estiri, H. / Castagna, R. / Parisini, E.
History
DepositionFeb 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1886
Polymers32,7591
Non-polymers4285
Water4,468248
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint1 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.876, 108.876, 35.402
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Leaf-branch compost cutinase / LC-cutinase / LCC / PET-digesting enzyme / Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase


Mass: 32759.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified prokaryotic organism (environmental samples)
Production host: Escherichia coli (E. coli)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Sodium citrate tribasic dihydrate 1M Isopropanol 20% PEG 4K 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7338 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7338 Å / Relative weight: 1
ReflectionResolution: 1.28→54.497 Å / Num. obs: 62178 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.998 / Net I/σ(I): 6.5
Reflection shellResolution: 1.28→1.302 Å / Num. unique obs: 3088 / CC1/2: 0.346

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→54.497 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.158 / SU B: 1.004 / SU ML: 0.04 / Average fsc free: 0.9649 / Average fsc work: 0.9697 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.048
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1871 3158 5.079 %
Rwork0.1634 59019 -
all0.165 --
obs-62177 99.998 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 13.685 Å2
Baniso -1Baniso -2Baniso -3
1-0.113 Å20.056 Å20 Å2
2--0.113 Å2-0 Å2
3----0.366 Å2
Refinement stepCycle: LAST / Resolution: 1.28→54.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 28 248 2246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0112093
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161954
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.6522867
X-RAY DIFFRACTIONr_angle_other_deg0.6121.5694493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5915277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.464519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82410310
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.891089
X-RAY DIFFRACTIONr_chiral_restr0.0960.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022529
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
X-RAY DIFFRACTIONr_nbd_refined0.2370.2413
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.21870
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21050
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2176
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.214
X-RAY DIFFRACTIONr_nbd_other0.1990.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.225
X-RAY DIFFRACTIONr_mcbond_it1.3971.2691051
X-RAY DIFFRACTIONr_mcbond_other1.3881.2681051
X-RAY DIFFRACTIONr_mcangle_it2.1522.2711317
X-RAY DIFFRACTIONr_mcangle_other2.1622.2761318
X-RAY DIFFRACTIONr_scbond_it2.3621.571042
X-RAY DIFFRACTIONr_scbond_other2.3611.5731043
X-RAY DIFFRACTIONr_scangle_it3.4652.7371540
X-RAY DIFFRACTIONr_scangle_other3.4632.7391541
X-RAY DIFFRACTIONr_lrange_it5.37217.5332440
X-RAY DIFFRACTIONr_lrange_other5.37117.5412441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.28-1.3130.3092380.32943600.32845980.9390.9290.334
1.313-1.3490.322410.30241660.30344070.9260.9330.307
1.349-1.3880.3022240.29341000.29443240.9360.9360.297
1.388-1.4310.2862030.25740050.25842080.9410.950.261
1.431-1.4780.242210.22838750.22940960.9570.9620.23
1.478-1.5290.2262020.20637440.20739460.9670.9720.205
1.529-1.5870.2091910.18736030.18837940.9720.9770.182
1.587-1.6520.231640.18235050.18436690.9680.9790.174
1.652-1.7250.2072010.1733110.17235120.9750.9830.159
1.725-1.8090.1841770.15832100.15933870.9780.9860.145
1.809-1.9070.1561660.14630490.14632150.9870.9880.133
1.907-2.0230.1781510.13728720.13930230.9810.9880.126
2.023-2.1620.1851400.1327280.13328680.9790.990.123
2.162-2.3350.1681240.13125500.13326740.9830.990.127
2.335-2.5570.1531200.13223390.13324590.9870.9890.131
2.557-2.8590.1731160.13221140.13422300.9830.9890.136
2.859-3.2990.179770.12919100.13119870.9830.990.135
3.299-4.0370.1251070.12815770.12816840.9920.9910.143
4.037-5.6940.143590.1312700.13113290.9890.9910.158
5.694-54.4970.168360.1697310.1697670.9940.9840.207

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