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- PDB-9um4: CaPETaseM9 SEC loop of 9CL variant -

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Basic information

Entry
Database: PDB / ID: 9um4
TitleCaPETaseM9 SEC loop of 9CL 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: 1.63 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
C: Cutinase
D: Cutinase


Theoretical massNumber of molelcules
Total (without water)114,4084
Polymers114,4084
Non-polymers00
Water6,161342
1
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,6021
Polymers28,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,6021
Polymers28,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,6021
Polymers28,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,6021
Polymers28,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.099, 74.498, 80.189
Angle α, β, γ (deg.)62.98, 87.75, 80.06
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cutinase


Mass: 28601.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CaPETaseM9 SEC loop of 9CL 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.: 342 / 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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.2M ammonium phosphate monobasic

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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: Nov 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 101820 / % possible obs: 95.9 % / Redundancy: 3.1 % / CC1/2: 0.99 / Net I/σ(I): 6.42
Reflection shellResolution: 1.63→1.69 Å / Rmerge(I) obs: 0.3223 / Num. unique obs: 9465

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YME

7yme


Resolution: 1.63→28.14 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.214 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21924 5047 5 %RANDOM
Rwork0.18322 ---
obs0.185 95888 95.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.75 Å2-0.51 Å2
2--0.98 Å2-0.15 Å2
3----0.76 Å2
Refinement stepCycle: 1 / Resolution: 1.63→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 0 342 8110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127944
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167201
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.78110860
X-RAY DIFFRACTIONr_angle_other_deg0.6081.73716549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81651007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.797556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82101120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021953
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_it2.1682.3414049
X-RAY DIFFRACTIONr_mcbond_other2.1662.3414049
X-RAY DIFFRACTIONr_mcangle_it3.1144.1895049
X-RAY DIFFRACTIONr_mcangle_other3.1154.195050
X-RAY DIFFRACTIONr_scbond_it2.8032.5893895
X-RAY DIFFRACTIONr_scbond_other2.8022.593896
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1194.6385812
X-RAY DIFFRACTIONr_long_range_B_refined5.38323.919100
X-RAY DIFFRACTIONr_long_range_B_other5.36523.799066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.633→1.675 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 343 -
Rwork0.267 6511 -
obs--86.54 %

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