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- PDB-8ytu: Mipa-PETase from Micromonospora pattaloongensis -

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Basic information

Entry
Database: PDB / ID: 8ytu
TitleMipa-PETase from Micromonospora pattaloongensis
Componentscutinase
KeywordsHYDROLASE / PET hydrolase
Function / homology: / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Cutinase
Function and homology information
Biological speciesMicromonospora pattaloongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsHong, H. / Seo, H. / Park, J. / Kim, K.-J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020M3A9I5037635 Korea, Republic Of
CitationJournal: Science / Year: 2025
Title: Landscape profiling of PET depolymerases using a natural sequence cluster framework.
Authors: Seo, H. / Hong, H. / Park, J. / Lee, S.H. / Ki, D. / Ryu, A. / Sagong, H.Y. / Kim, K.J.
History
DepositionMar 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cutinase
B: cutinase
C: cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0055
Polymers83,8503
Non-polymers1542
Water8,701483
1
A: cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0122
Polymers27,9501
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint0 kcal/mol
Surface area9280 Å2
MethodPISA
2
B: cutinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0422
Polymers27,9501
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9470 Å2
MethodPISA
3
C: cutinase


Theoretical massNumber of molelcules
Total (without water)27,9501
Polymers27,9501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.067, 103.411, 131.875
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 / Recombinant Mipa-PETase


Mass: 27950.119 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora pattaloongensis (bacteria)
Gene: SAMN05444365_106119 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -T1R / References: UniProt: A0A1H3QT72, cutinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / 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 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 / Details: PEG 8000, CAPS

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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: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2020
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.34→36.82 Å / Num. obs: 136706 / % possible obs: 96.1 % / Redundancy: 2.6 % / CC1/2: 0.99 / Net I/σ(I): 0.364
Reflection shellResolution: 1.34→1.41 Å / Num. unique obs: 115359 / CC1/2: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→36.82 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.868 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23437 7442 5.2 %RANDOM
Rwork0.21079 ---
obs0.21202 136706 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å20 Å2
2--0.87 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.34→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5675 0 10 483 6168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0115922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165322
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.6428100
X-RAY DIFFRACTIONr_angle_other_deg0.5141.56412205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.59552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03810790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2868
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027304
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021500
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_it1.9632.3013099
X-RAY DIFFRACTIONr_mcbond_other1.9612.3013099
X-RAY DIFFRACTIONr_mcangle_it2.7434.1253886
X-RAY DIFFRACTIONr_mcangle_other2.7434.1273887
X-RAY DIFFRACTIONr_scbond_it2.6642.5752823
X-RAY DIFFRACTIONr_scbond_other2.6632.5782824
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0654.5954215
X-RAY DIFFRACTIONr_long_range_B_refined5.8724.676697
X-RAY DIFFRACTIONr_long_range_B_other5.73923.316589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.343→1.378 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.478 356 -
Rwork0.492 6109 -
obs--58.87 %

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