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- PDB-8ytv: The M19 variant of Mipa-Petase from Micromonospora pattaloongensis -

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Basic information

Entry
Database: PDB / ID: 8ytv
TitleThe M19 variant of Mipa-Petase from Micromonospora pattaloongensis
Componentscutinase
KeywordsHYDROLASE / PET hydrolase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / Cutinase
Function and homology information
Biological speciesMicromonospora pattaloongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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


Theoretical massNumber of molelcules
Total (without water)56,5262
Polymers56,5262
Non-polymers00
Water3,297183
1
A: cutinase


Theoretical massNumber of molelcules
Total (without water)28,2631
Polymers28,2631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cutinase


Theoretical massNumber of molelcules
Total (without water)28,2631
Polymers28,2631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.619, 51.359, 107.654
Angle α, β, γ (deg.)90.00, 94.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cutinase / Recombinant Mipa-P-M19 variant


Mass: 28262.830 Da / Num. of mol.: 2
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): Rosetta Gami-B / References: UniProt: A0A1H3QT72, cutinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: PET3350, Citric acid, BIS-Tris propane

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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 EIGER X 9M / Detector: PIXEL / Date: Jan 4, 2024
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: 1.89→42.5 Å / Num. obs: 35259 / % possible obs: 99.7 % / Redundancy: 8.6 % / CC1/2: 0.98 / Net I/σ(I): 7.9
Reflection shellResolution: 1.89→2.01 Å / Num. unique obs: 35259 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→38.56 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.647 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24145 1928 5.2 %RANDOM
Rwork0.18833 ---
obs0.19114 35259 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.828 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å20.49 Å2
2---2.99 Å2-0 Å2
3---4.15 Å2
Refinement stepCycle: 1 / Resolution: 1.89→38.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 0 183 3919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0113924
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163536
X-RAY DIFFRACTIONr_angle_refined_deg1.291.6385369
X-RAY DIFFRACTIONr_angle_other_deg0.4271.5618120
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.107531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24110543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
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_it2.3783.1672052
X-RAY DIFFRACTIONr_mcbond_other2.3783.1672052
X-RAY DIFFRACTIONr_mcangle_it3.4055.6852572
X-RAY DIFFRACTIONr_mcangle_other3.4045.6852573
X-RAY DIFFRACTIONr_scbond_it3.3443.4771872
X-RAY DIFFRACTIONr_scbond_other3.3383.4751871
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9026.2592798
X-RAY DIFFRACTIONr_long_range_B_refined6.67132.724440
X-RAY DIFFRACTIONr_long_range_B_other6.66432.434423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.893→1.942 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 122 -
Rwork0.344 2533 -
obs--97.07 %

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