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- PDB-9um6: CaPETaseM9 SEC loop of 10CL+E289P variant -

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Basic information

Entry
Database: PDB / ID: 9um6
TitleCaPETaseM9 SEC loop of 10CL+E289P 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: 1.66 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)57,7972
Polymers57,7972
Non-polymers00
Water3,747208
1
A: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,8981
Polymers28,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cutinase


Theoretical massNumber of molelcules
Total (without water)28,8981
Polymers28,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.134, 116.359, 142.276
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: 28898.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CaPETaseM9 SEC loop of 10CL+E289P 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.: 208 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% (w/v) PEG 3350, 4% (v/v) tacsimate pH 4.0

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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: 1.66→50 Å / Num. obs: 81578 / % possible obs: 99.9 % / Redundancy: 12.5 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.043 / Rrim(I) all: 0.155 / Χ2: 3.885 / Net I/σ(I): 10.8 / Num. measured all: 1017168
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.66-1.699.40.49139910.9060.9750.1670.520.66599.5
1.69-1.72100.43540160.8990.9730.1440.4590.77499.7
1.72-1.7510.60.41939800.9480.9870.1370.4410.8999.9
1.75-1.7911.40.35940860.9570.9890.1110.3761.14599.9
1.79-1.8312.50.34240100.9680.9920.0990.3561.264100
1.83-1.8713.40.31140310.9730.9930.0870.3241.655100
1.87-1.9213.50.2839970.9670.9920.0790.2911.841100
1.92-1.9713.40.24740740.9810.9950.070.2571.98100
1.97-2.0313.30.23340150.9840.9960.0660.2422.315100
2.03-2.0913.20.21440650.9840.9960.060.2222.821100
2.09-2.1712.90.18740910.9830.9960.0540.1943.488100
2.17-2.2512.10.18339990.9880.9970.0550.1913.358100
2.25-2.3613.40.19440810.990.9980.0550.2024.008100
2.36-2.4813.20.16540740.990.9980.0460.1724.476100
2.48-2.6312.40.15840800.9890.9970.0460.1655.333100
2.63-2.8413.60.15341100.9910.9980.0430.1595.789100
2.84-3.1213.50.15141160.9940.9990.0420.1576.766100
3.12-3.58130.12241470.9940.9980.0350.1278.207100
3.58-4.512.30.12742100.9950.9990.0370.1338.917100
4.5-5012.20.11244050.9950.9990.0330.1178.98799.6

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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: 1.66→34.08 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.522 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20891 4060 5 %RANDOM
Rwork0.185 ---
obs0.18621 77432 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.66→34.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3945 0 0 208 4153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124064
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163684
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.7855560
X-RAY DIFFRACTIONr_angle_other_deg0.6911.7348472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.455530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20910565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
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_it2.0791.92074
X-RAY DIFFRACTIONr_mcbond_other2.0781.92074
X-RAY DIFFRACTIONr_mcangle_it2.8363.4142589
X-RAY DIFFRACTIONr_mcangle_other2.8363.4152590
X-RAY DIFFRACTIONr_scbond_it2.8282.1561990
X-RAY DIFFRACTIONr_scbond_other2.8282.1571991
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1763.8362972
X-RAY DIFFRACTIONr_long_range_B_refined4.91720.034530
X-RAY DIFFRACTIONr_long_range_B_other4.91219.824506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.661→1.704 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 282 -
Rwork0.211 5575 -
obs--98.6 %

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