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- PDB-8z2g: MHET bound form of PET-degrading cutinase mutant Cut190*SS_S176A -

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Basic information

Entry
Database: PDB / ID: 8z2g
TitleMHET bound form of PET-degrading cutinase mutant Cut190*SS_S176A
ComponentsAlpha/beta hydrolase family protein
KeywordsHYDROLASE / PROTEIN ENGINEERING / POLYESTERASE / METAL BINDING / Aromatic ligand
Function / homologyPlatelet-activating factor acetylhydrolase, isoform II / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / metal ion binding / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / AMMONIUM ION / Cutinase
Function and homology information
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNumoto, N. / Kondo, F. / Bekker, G.J. / Liao, Z. / Yamashita, M. / Iida, A. / Ito, N. / Kamiya, N. / Oda, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP21H02120 Japan
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity.
Authors: Numoto, N. / Kondo, F. / Bekker, G.J. / Liao, Z. / Yamashita, M. / Iida, A. / Ito, N. / Kamiya, N. / Oda, M.
History
DepositionApr 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)58,5197
Polymers57,7792
Non-polymers7405
Water4,648258
1
A: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3274
Polymers28,8901
Non-polymers4373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1923
Polymers28,8901
Non-polymers3022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.025, 83.025, 64.501
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Space group name HallP3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 28889.537 Da / Num. of mol.: 2 / Mutation: Q123H/Q138A/S176A/N202H/S226P/R228S/D250C/E296C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, SAMN02982918_2340 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B(DE3) / References: UniProt: W0TJ64, cutinase

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Non-polymers , 5 types, 263 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical ChemComp-C9C / 4-(2-hydroxyethyloxycarbonyl)benzoic acid / monohydroxyethyl terephthalate


Mass: 210.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.13 M Ammonium sulfate, 0.66 M MES pH 6.5, 20% (w/v) PEG monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→48.01 Å / Num. obs: 39011 / % possible obs: 99.1 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rsym value: 0.124 / Net I/σ(I): 6.9
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6294 / CC1/2: 0.633 / Rsym value: 0.663 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CTS

7cts


Resolution: 1.9→48.01 Å / Cross valid method: FREE R-VALUE / σ(F): 64.41 / Phase error: 35.3033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2028 1961 5.03 %
Rwork0.1752 37045 -
obs0.2019 39006 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4010 0 51 258 4319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00234172
X-RAY DIFFRACTIONf_angle_d0.53375679
X-RAY DIFFRACTIONf_chiral_restr0.0419606
X-RAY DIFFRACTIONf_plane_restr0.0055744
X-RAY DIFFRACTIONf_dihedral_angle_d12.65281540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.27161430.27892630X-RAY DIFFRACTION93.36
1.95-20.34381360.28112633X-RAY DIFFRACTION95.02
2-2.060.30081420.27412674X-RAY DIFFRACTION94.89
2.06-2.120.31081440.27022695X-RAY DIFFRACTION94.86
2.12-2.20.27211390.26562666X-RAY DIFFRACTION95.04
2.2-2.290.31161460.24982676X-RAY DIFFRACTION94.63
2.29-2.390.25591440.23732644X-RAY DIFFRACTION94.5
2.39-2.520.25641310.23232646X-RAY DIFFRACTION94.7
2.52-2.670.26561380.22332662X-RAY DIFFRACTION94.6
2.67-2.880.21051400.20652639X-RAY DIFFRACTION94.22
2.88-3.170.23631260.19972630X-RAY DIFFRACTION93.3
3.17-3.630.19751420.19352636X-RAY DIFFRACTION93.54
3.63-4.570.19891420.15172579X-RAY DIFFRACTION91.16
4.57-48.010.18831390.14742644X-RAY DIFFRACTION94.43

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