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- PDB-9qyr: Crystal structure of leaf branch compost cutinase variant ICCG L5... -

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Basic information

Entry
Database: PDB / ID: 9qyr
TitleCrystal structure of leaf branch compost cutinase variant ICCG L50Y Q183K
ComponentsLeaf-branch compost cutinase
KeywordsHYDROLASE / cutinase / PET depolymerase
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / cutinase / cutinase activity / extracellular region
Similarity search - Function
Alpha/beta hydrolase fold-5 / Alpha/beta hydrolase family / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Leaf-branch compost cutinase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsBischoff, D. / Walla, B. / Janowski, R. / Niessing, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE2715/14-2 Germany
CitationJournal: Bioengineering / Year: 2025
Title: Application of a Rational Crystal Contact Engineering Strategy on a Poly(ethylene terephthalate)-Degrading Cutinase
Authors: Walla, B. / Dietrich, A.M. / Brames, E. / Bischoff, D. / Fritzsche, S. / Castiglione, K. / Janowski, R. / Niessing, D. / Weuster-Botz, D.
History
DepositionApr 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: 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)28,9883
Polymers28,9171
Non-polymers712
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area9820 Å2
Unit cell
Length a, b, c (Å)96.57, 96.57, 73.16
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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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: 28917.379 Da / Num. of mol.: 1 / Mutation: L50Y Q183K
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 10 mM Tris, 150 mM NaCl, 0.6 M succinic acid, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→48.29 Å / Num. obs: 964320 / % possible obs: 99.5 % / Redundancy: 25.93 % / CC1/2: 0.806 / Net I/σ(I): 19.09
Reflection shellResolution: 1.71→1.81 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 152116 / CC1/2: 0.806 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSJun 30, 2024data reduction
XDSJun 30, 2024data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→48.285 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.151 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.089 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2038 1891 5.002 %
Rwork0.1713 35916 -
all0.173 --
obs-37807 99.636 %
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: 30.692 Å2
Baniso -1Baniso -2Baniso -3
1--0.408 Å20 Å20 Å2
2---0.408 Å20 Å2
3---0.816 Å2
Refinement stepCycle: LAST / Resolution: 1.71→48.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 2 292 2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122047
X-RAY DIFFRACTIONr_angle_refined_deg1.981.7842808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0135266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.164518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.12310293
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.7111087
X-RAY DIFFRACTIONr_chiral_restr0.1350.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021615
X-RAY DIFFRACTIONr_nbd_refined0.2150.2986
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3690.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3550.215
X-RAY DIFFRACTIONr_mcbond_it2.6712.7661052
X-RAY DIFFRACTIONr_mcangle_it3.3024.9551322
X-RAY DIFFRACTIONr_scbond_it3.9382.986995
X-RAY DIFFRACTIONr_scangle_it4.9845.3771486
X-RAY DIFFRACTIONr_lrange_it7.09631.483313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.71-1.7540.4311330.41825310.41927690.940.93896.2080.408
1.754-1.8020.3451330.30725220.30926650.9540.95599.62480.283
1.802-1.8550.2961310.23624880.23926210.9450.96399.92370.203
1.855-1.9120.2391270.20824060.20925330.9650.9691000.18
1.912-1.9740.241230.20223460.20424690.960.9721000.175
1.974-2.0430.2131200.17522850.17724050.9690.9811000.15
2.043-2.120.2081150.17521850.17623000.9730.981000.15
2.12-2.2070.1831120.16621160.16722280.9750.9821000.141
2.207-2.3050.2091070.16720330.16921410.9730.98299.95330.145
2.305-2.4170.2421030.16619560.1720590.9630.9821000.145
2.417-2.5470.219970.17818510.18119490.9720.9899.94870.157
2.547-2.7010.205930.17117610.17318580.9780.98299.78470.154
2.701-2.8870.18870.17216570.17317480.9760.98199.77120.159
2.887-3.1180.21820.19215600.19316480.9710.97699.63590.182
3.118-3.4140.221750.17714250.17915000.9720.9821000.177
3.414-3.8140.201700.16713180.16913880.9770.9851000.173
3.814-4.40.146610.12311750.12412360.990.9921000.133
4.4-5.3770.177530.12410050.12610580.9830.9911000.138
5.377-7.5580.187430.168040.1628480.9830.98899.88210.177
7.558-48.2850.162260.1584920.1595190.9880.98599.80730.196

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