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- PDB-9um8: CaPETaseM9 + P289E variant -

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Basic information

Entry
Database: PDB / ID: 9um8
TitleCaPETaseM9 + P289E variant
ComponentsCutinase
KeywordsHYDROLASE / PETase / Cryptosporangium / aurantiacum / CaPETase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / PET hydrolase/cutinase-like domain-containing protein
Function and homology information
Biological speciesCryptosporangium aurantiacum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsKim, K. / Ki, D. / Park, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mechanistic Insights into Modulation of Productive Substrate Accessibility for Efficient PET Depolymerization
Authors: Kim, K. / Ki, D. / Park, J.
History
DepositionApr 21, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cutinase
B: Cutinase


Theoretical massNumber of molelcules
Total (without water)56,7162
Polymers56,7162
Non-polymers00
Water5,350297
1
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,3581
Polymers28,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,3581
Polymers28,3581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.990, 112.019, 113.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cutinase


Mass: 28357.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CaPETaseM9 P289E variant
Source: (gene. exp.) Cryptosporangium aurantiacum (bacteria)
Gene: SAMN05443668_101498 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1M7II12
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.04M Citricacid, 0.06 M BIS-TRIS propane pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 145353 / % possible obs: 93.5 % / Redundancy: 7.4 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.037 / Rrim(I) all: 0.12 / Χ2: 8.648 / Net I/σ(I): 16.2 / Num. measured all: 1071403
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.22-1.244.70.4765790.7640.9310.2180.521.35284.8
1.24-1.265.40.46966330.7830.9370.2050.5141.47987
1.26-1.295.80.46167290.8230.950.1910.5011.76587.3
1.29-1.316.40.4568170.8520.9590.1740.4842.21288.8
1.31-1.346.90.42367960.8380.9550.1550.4522.4588.7
1.34-1.376.90.39768570.8650.9630.1460.4242.65788.8
1.37-1.416.70.36268520.8980.9730.1350.3882.80189
1.41-1.456.60.33168790.9050.9750.1240.3553.36789.3
1.45-1.496.40.29869640.9240.980.1140.323.94190.2
1.49-1.546.10.26470700.9370.9840.1040.2854.73991.6
1.54-1.596.30.24273260.9460.9860.0940.2615.79794.7
1.59-1.666.60.22373960.9590.9890.0850.246.43895.7
1.66-1.736.50.275750.9630.9910.0790.2167.42597.5
1.73-1.826.80.18375550.970.9920.0710.1979.56497.8
1.82-1.947.70.1777340.9780.9940.0620.18211.79299
1.94-2.098.20.15477420.9820.9960.0550.16314.18399.5
2.09-2.38.70.13878050.9870.9970.0480.14615.0299.5
2.3-2.638.90.11978400.990.9970.0410.12614.93399.7
2.63-3.3111.30.10379580.9950.9990.0310.10814.704100
3.31-5012.50.08482460.9970.9990.0240.08714.52399.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YME

7yme


Resolution: 1.22→33.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.593 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19077 7306 5 %RANDOM
Rwork0.17528 ---
obs0.17606 137968 93.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.22→33.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 0 297 4273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124074
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163687
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.7845574
X-RAY DIFFRACTIONr_angle_other_deg0.6851.7318480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.837528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62910567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2571.1542082
X-RAY DIFFRACTIONr_mcbond_other1.2571.1542082
X-RAY DIFFRACTIONr_mcangle_it1.8182.0762599
X-RAY DIFFRACTIONr_mcangle_other1.822.0772600
X-RAY DIFFRACTIONr_scbond_it2.2151.351992
X-RAY DIFFRACTIONr_scbond_other2.2151.3511993
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2282.3932976
X-RAY DIFFRACTIONr_long_range_B_refined3.70312.194520
X-RAY DIFFRACTIONr_long_range_B_other3.67711.74480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.221→1.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 440 -
Rwork0.239 9096 -
obs--83.88 %

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