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- PDB-8ytz: The P185V variant of Kubu-PETase from Kutzneria buriramensis -

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Basic information

Entry
Database: PDB / ID: 8ytz
TitleThe P185V variant of Kubu-PETase from Kutzneria buriramensis
ComponentsDienelactone hydrolase
KeywordsHYDROLASE / PET hydrolase
Function / homologyChlorophyllase / Chlorophyllase / carboxylic ester hydrolase activity / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha/Beta hydrolase fold / ACETATE ION / Dienelactone hydrolase
Function and homology information
Biological speciesKutzneria buriramensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPark, J. / Seo, H. / Hong, H. / 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

Downloads & links

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Assembly

Deposited unit
A: Dienelactone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,35618
Polymers26,9361
Non-polymers1,42017
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.219, 157.219, 157.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

21A-586-

HOH

31A-593-

HOH

41A-594-

HOH

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Components

#1: Protein Dienelactone hydrolase


Mass: 26936.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kutzneria buriramensis (bacteria) / Gene: BCF44_11928 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -T1R / References: UniProt: A0A3E0H050
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.01 Å3/Da / Density % sol: 59.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 300, imidazole, zinc acetate

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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: Jun 24, 2023
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: 1.7→42.03 Å / Num. obs: 34762 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.99 / Net I/σ(I): 28
Reflection shellResolution: 1.7→1.78 Å / Num. unique obs: 13297 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.34 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.697 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19545 1801 4.9 %RANDOM
Rwork0.16143 ---
obs0.16312 34762 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.981 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.7→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 57 197 2074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121921
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161762
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.6372615
X-RAY DIFFRACTIONr_angle_other_deg0.5821.5574038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7085250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.6259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86410235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
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_it2.6832.6681012
X-RAY DIFFRACTIONr_mcbond_other2.5512.6361003
X-RAY DIFFRACTIONr_mcangle_it3.394.721252
X-RAY DIFFRACTIONr_mcangle_other3.4024.7221253
X-RAY DIFFRACTIONr_scbond_it3.9143.022909
X-RAY DIFFRACTIONr_scbond_other3.9133.022910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7025.3551364
X-RAY DIFFRACTIONr_long_range_B_refined7.51428.072265
X-RAY DIFFRACTIONr_long_range_B_other7.46727.222229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 122 -
Rwork0.279 2565 -
obs--100 %

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