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- PDB-8ota: High resolution crystal structure of a Leaf-branch compost cutina... -

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Basic information

Entry
Database: PDB / ID: 8ota
TitleHigh resolution crystal structure of a Leaf-branch compost cutinase quadruple variant
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / SERINE ESTERASE / CUTINASE
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function
Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Leaf-branch compost cutinase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGavalda, S. / Cioci, G. / Marty, A. / Duquesne, S.
Funding support France, 1items
OrganizationGrant numberCountry
French National Institute of Agricultural Research (INRAE) France
CitationJournal: Biophys.J. / Year: 2024
Title: Exploring the pH dependence of an improved PETase.
Authors: Charlier, C. / Gavalda, S. / Grga, J. / Perrot, L. / Gabrielli, V. / Lohr, F. / Schorghuber, J. / Lichtenecker, R. / Arnal, G. / Marty, A. / Tournier, V. / Lippens, G.
History
DepositionApr 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8832
Polymers27,7951
Non-polymers881
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint3 kcal/mol
Surface area9910 Å2
Unit cell
Length a, b, c (Å)110.184, 110.184, 35.582
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-766-

HOH

21A-768-

HOH

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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: 27795.168 Da / Num. of mol.: 1 / Mutation: F243I, D238C, S283C, Y127G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G9BY57, cutinase, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bicine pH9, 10% PEG20000, 2% dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.719→36.07 Å / Num. obs: 26667 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 19.53 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.9
Reflection shellResolution: 1.719→1.749 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1350 / CC1/2: 0.774 / Rpim(I) all: 0.273 / Rrim(I) all: 0.706 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→36.07 Å / SU ML: 0.2448 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.4438
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2035 1407 5.28 %
Rwork0.173 25260 -
obs0.1746 26667 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.22 Å2
Refinement stepCycle: LAST / Resolution: 1.72→36.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1949 0 6 369 2324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722048
X-RAY DIFFRACTIONf_angle_d0.85092815
X-RAY DIFFRACTIONf_chiral_restr0.0596319
X-RAY DIFFRACTIONf_plane_restr0.0086371
X-RAY DIFFRACTIONf_dihedral_angle_d5.8974306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.780.4271490.3482530X-RAY DIFFRACTION99.96
1.78-1.850.25471360.22422490X-RAY DIFFRACTION100
1.85-1.940.22341320.17272503X-RAY DIFFRACTION100
1.94-2.040.16561320.15232498X-RAY DIFFRACTION100
2.04-2.170.20971240.18182523X-RAY DIFFRACTION100
2.17-2.330.18321390.14362519X-RAY DIFFRACTION100
2.33-2.570.20731530.17152512X-RAY DIFFRACTION100
2.57-2.940.20011380.16282526X-RAY DIFFRACTION100
2.94-3.70.20781240.17312557X-RAY DIFFRACTION100
3.7-100.18281800.16422602X-RAY DIFFRACTION100

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