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- PDB-6ths: High resolution crystal structure of Leaf-branch cutinase S165A v... -

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Basic information

Entry
Database: PDB / ID: 6ths
TitleHigh resolution crystal structure of Leaf-branch cutinase S165A variant
ComponentsLCC
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
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 / molecular replacement / Resolution: 1.1 Å
AuthorsNomme, J.
CitationJournal: Nature / Year: 2020
Title: An engineered PET depolymerase to break down and recycle plastic bottles.
Authors: Tournier, V. / Topham, C.M. / Gilles, A. / David, B. / Folgoas, C. / Moya-Leclair, E. / Kamionka, E. / Desrousseaux, M.L. / Texier, H. / Gavalda, S. / Cot, M. / Guemard, E. / Dalibey, M. / ...Authors: Tournier, V. / Topham, C.M. / Gilles, A. / David, B. / Folgoas, C. / Moya-Leclair, E. / Kamionka, E. / Desrousseaux, M.L. / Texier, H. / Gavalda, S. / Cot, M. / Guemard, E. / Dalibey, M. / Nomme, J. / Cioci, G. / Barbe, S. / Chateau, M. / Andre, I. / Duquesne, S. / Marty, A.
History
DepositionNov 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / 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: LCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8722
Polymers27,7841
Non-polymers881
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint3 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.604, 109.604, 35.287
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 LCC


Mass: 27783.992 Da / Num. of mol.: 1 / Mutation: S165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Plasmid: pET26b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9BY57, cutinase
#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.: 290 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 285 K / Method: vapor diffusion / pH: 9 / Details: 0.1 M Bicine pH 9.0, 2% Dioxane, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97907 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.1→47.51 Å / Num. obs: 98700 / % possible obs: 99.6 % / Redundancy: 12.711 % / Biso Wilson estimate: 15.012 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.07 / Χ2: 1.152 / Net I/σ(I): 18.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.1611.9130.5853.27155160.9140.61197.5
1.16-1.2412.6390.4195.06149710.9550.437100
1.24-1.3412.9480.2997.37139680.9780.312100
1.34-1.4713.1090.19711.51128630.9910.205100
1.47-1.6513.3410.12419.41116510.9960.129100
1.65-1.912.7560.08728.3102990.9980.091100
1.9-2.3312.4730.06439.6187530.9990.066100
2.33-3.2912.4860.05148.268150.9990.053100
3.29-47.5112.9390.04154.7938640.9990.04399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EB0

4eb0


Resolution: 1.1→47.51 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 2.066 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1671 4397 5 %RANDOM
Rwork0.1362 ---
obs0.1377 83724 88.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.19 Å2 / Biso mean: 15.091 Å2 / Biso min: 9 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----3.03 Å2
Refinement stepCycle: final / Resolution: 1.1→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 6 290 2257
Biso mean--14.45 28.84 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0142047
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171761
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.6572811
X-RAY DIFFRACTIONr_angle_other_deg1.1621.6344136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5945269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86720.777103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.9915290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9891516
X-RAY DIFFRACTIONr_chiral_restr0.1070.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022369
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02391
X-RAY DIFFRACTIONr_rigid_bond_restr4.64432047
X-RAY DIFFRACTIONr_sphericity_free24.2045189
X-RAY DIFFRACTIONr_sphericity_bonded16.92352089
LS refinement shellResolution: 1.1→1.127 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.307 283 -
Rwork0.284 5103 -
obs--74.26 %

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