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- PDB-7cef: Crystal structure of PET-degrading cutinase Cut190 /S226P/R228S/ ... -

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Basic information

Entry
Database: PDB / ID: 7cef
TitleCrystal structure of PET-degrading cutinase Cut190 /S226P/R228S/ mutant with the C-terminal three residues deletion
ComponentsAlpha/beta hydrolase family protein
KeywordsHYDROLASE / PROTEIN ENGINEERING / THERMOSTABILITY / POLYESTERASE / Multiple conformation
Function / homologyPlatelet-activating factor acetylhydrolase, isoform II / cutinase / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / cutinase
Function and homology information
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSenga, A. / Numoto, N. / Ito, N. / Kawai, F. / Oda, M.
CitationJournal: J.Biochem. / Year: 2021
Title: Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability.
Authors: Senga, A. / Numoto, N. / Yamashita, M. / Iida, A. / Ito, N. / Kawai, F. / Oda, M.
History
DepositionJun 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 7, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase family protein
B: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,85820
Polymers57,7062
Non-polymers1,15218
Water12,719706
1
A: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3519
Polymers28,8531
Non-polymers4988
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-198 kcal/mol
Surface area10430 Å2
MethodPISA
2
B: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,50711
Polymers28,8531
Non-polymers65410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-180 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.512, 49.100, 82.948
Angle α, β, γ (deg.)90.000, 107.453, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Alpha/beta hydrolase family protein / Cutinase


Mass: 28853.221 Da / Num. of mol.: 2 / Mutation: S226P/R228S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, SAMN02982918_2340 / Production host: Escherichia coli (E. coli) / References: UniProt: W0TJ64, cutinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.04 Å3/Da / Density % sol: 39.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M zinc acetate, 0.1M sodium cacodylate, 18% PEG 8000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 60359 / % possible obs: 97.8 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.55 Å2 / CC1/2: 0.995 / Rsym value: 0.083 / Net I/σ(I): 9.3
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 9640 / CC1/2: 0.742 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFI, 4WFJ

4wfi

4wfj


Resolution: 1.6→41.72 Å / SU ML: 0.1956 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4566 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 3017 5 %Random selection
Rwork0.1768 57319 --
obs0.1789 60336 97.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.99 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 18 706 4792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784180
X-RAY DIFFRACTIONf_angle_d0.92775698
X-RAY DIFFRACTIONf_chiral_restr0.0581610
X-RAY DIFFRACTIONf_plane_restr0.0073758
X-RAY DIFFRACTIONf_dihedral_angle_d10.43122502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.29011500.27232534X-RAY DIFFRACTION96.69
1.62-1.650.28931400.26012557X-RAY DIFFRACTION97.22
1.65-1.680.33231200.26222596X-RAY DIFFRACTION97.1
1.68-1.710.271370.25212543X-RAY DIFFRACTION97.38
1.71-1.740.29671280.24462609X-RAY DIFFRACTION97.44
1.74-1.780.31391330.23042582X-RAY DIFFRACTION97.14
1.78-1.820.27781460.22432575X-RAY DIFFRACTION97.46
1.82-1.860.2751380.21482580X-RAY DIFFRACTION97.31
1.86-1.910.29321290.19452539X-RAY DIFFRACTION96.88
1.91-1.960.22991440.1912601X-RAY DIFFRACTION97.62
1.96-2.010.23121310.18232591X-RAY DIFFRACTION97.81
2.01-2.080.24041240.17612626X-RAY DIFFRACTION98.43
2.08-2.150.22911510.17632611X-RAY DIFFRACTION98.64
2.15-2.240.2071360.16882646X-RAY DIFFRACTION98.58
2.24-2.340.23041320.16842636X-RAY DIFFRACTION98.96
2.34-2.470.25331450.16422594X-RAY DIFFRACTION99.06
2.47-2.620.19581310.16542643X-RAY DIFFRACTION98.09
2.62-2.820.19581350.17352611X-RAY DIFFRACTION98.53
2.82-3.110.2351440.17072640X-RAY DIFFRACTION97.92
3.11-3.560.18391380.15592656X-RAY DIFFRACTION98.69
3.56-4.480.16861460.13812648X-RAY DIFFRACTION98.38
4.48-41.720.19131390.17192701X-RAY DIFFRACTION97.33

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