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- PDB-9qyu: Crystal structure of leaf branch compost cutinase quintuple varia... -

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Basic information

Entry
Database: PDB / ID: 9qyu
TitleCrystal structure of leaf branch compost cutinase quintuple variant ICCG L50Y
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: 1.51 Å
AuthorsBischoff, D. / Walla, B. / Dietrich, A.-M. / 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 21, 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
B: Leaf-branch compost cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9948
Polymers27,5861
Non-polymers4087
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint3 kcal/mol
Surface area9930 Å2
Unit cell
Length a, b, c (Å)96.65, 96.65, 73.71
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: 27585.861 Da / Num. of mol.: 1
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.12 Å3/Da / Density % sol: 60.58 %
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 PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→48.56 Å / Num. obs: 1098150 / % possible obs: 100 % / Redundancy: 19.88 % / CC1/2: 1 / Net I/σ(I): 25.82
Reflection shellResolution: 1.51→1.6 Å / Num. unique obs: 8798 / CC1/2: 0.678

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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: 1.51→48.325 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.099 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.058 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.1836 2763 5.002 %
Rwork0.1494 52479 -
all0.151 --
obs-55242 99.987 %
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: 33.521 Å2
Baniso -1Baniso -2Baniso -3
1-1.121 Å2-0 Å2-0 Å2
2--1.121 Å2-0 Å2
3----2.243 Å2
Refinement stepCycle: LAST / Resolution: 1.51→48.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1943 0 25 205 2173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122045
X-RAY DIFFRACTIONr_angle_refined_deg1.591.7872791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6355262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.004517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.78710288
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.2741086
X-RAY DIFFRACTIONr_chiral_restr0.1050.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021595
X-RAY DIFFRACTIONr_nbd_refined0.2110.2969
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2153
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it6.6253.041042
X-RAY DIFFRACTIONr_mcangle_it8.8095.481306
X-RAY DIFFRACTIONr_scbond_it9.3633.2941003
X-RAY DIFFRACTIONr_scangle_it11.8355.9621485
X-RAY DIFFRACTIONr_lrange_it15.37834.2723192
X-RAY DIFFRACTIONr_rigid_bond_restr5.07832045
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
1.51-1.5490.3412010.30138050.30340080.9410.96399.95010.304
1.549-1.5910.3081960.26737200.26939160.9450.9731000.267
1.591-1.6380.2631910.24636400.24738310.9720.9771000.238
1.638-1.6880.241860.19235380.19437240.9730.9871000.178
1.688-1.7430.2011790.17134010.17235800.9770.9891000.151
1.743-1.8040.1831750.13833140.1434890.9810.9921000.116
1.804-1.8720.1651690.11132130.11433820.9830.9941000.09
1.872-1.9490.1531610.10130610.10432220.9870.9951000.083
1.949-2.0350.161560.1129690.11231250.9850.9941000.096
2.035-2.1340.1661500.12228510.12430020.9850.99399.96670.108
2.134-2.2490.1861430.12927070.13228500.9790.9911000.117
2.249-2.3860.161350.1225650.12227010.9820.99399.9630.111
2.386-2.550.1921270.13324190.13625460.9760.991000.127
2.55-2.7530.1861200.15122690.15323890.9810.9871000.147
2.753-3.0150.1961090.15820750.1621840.9760.9851000.16
3.015-3.370.2081000.16719150.16920150.9760.9841000.178
3.37-3.8880.172900.15717020.15817920.980.9861000.178
3.888-4.7540.13760.11914480.11915240.990.9921000.145
4.754-6.690.218620.16811640.17112260.9790.9871000.206
6.69-48.3250.184370.1837030.1837400.9890.9861000.243

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