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- PDB-8z2j: Substrate analog a012 bound form of PET-degrading cutinase mutant... -

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Basic information

Entry
Database: PDB / ID: 8z2j
TitleSubstrate analog a012 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 / : / ACETATE ION / Cutinase
Function and homology information
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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

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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)58,38815
Polymers57,0662
Non-polymers1,32213
Water10,971609
1
A: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1176
Polymers28,5331
Non-polymers5845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2719
Polymers28,5331
Non-polymers7388
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.560, 78.840, 74.250
Angle α, β, γ (deg.)90.000, 106.122, 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

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Protein , 1 types, 2 molecules AB

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


Mass: 28533.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Gene: Cut190, MINT15_00360 / 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 , 6 types, 622 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-A1L0M / (4-methoxycarbonylphenyl)-(2-phenylmethoxyethoxy)phosphinic acid


Mass: 350.303 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.05 Å3/Da / Density % sol: 39.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.2 M NaCl, 0.1 M Sodium acetate trihydrate pH 4.6, 30% (v/v) 2-Methyl-2,4-pentanediol, and 2 mM ligand

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→40 Å / Num. obs: 36906 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 13.33 Å2 / CC1/2: 0.983 / Rsym value: 0.445 / Net I/σ(I): 7.6
Reflection shellResolution: 1.89→2 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5712 / CC1/2: 0.582 / Rsym value: 2

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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: 1.89→39.93 Å / SU ML: 0.2123 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.1047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2074 1853 5.02 %
Rwork0.1594 35024 -
obs0.1618 36877 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.73 Å2
Refinement stepCycle: LAST / Resolution: 1.89→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4012 0 79 609 4700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674203
X-RAY DIFFRACTIONf_angle_d0.8615727
X-RAY DIFFRACTIONf_chiral_restr0.0538611
X-RAY DIFFRACTIONf_plane_restr0.0089750
X-RAY DIFFRACTIONf_dihedral_angle_d14.51231559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.26551430.22022665X-RAY DIFFRACTION99.82
1.94-20.27731390.21672673X-RAY DIFFRACTION100
2-2.060.27381390.20352701X-RAY DIFFRACTION99.96
2.06-2.140.291430.19292672X-RAY DIFFRACTION100
2.14-2.220.23821390.18082675X-RAY DIFFRACTION100
2.22-2.320.20421420.16842711X-RAY DIFFRACTION100
2.32-2.450.20561410.16062681X-RAY DIFFRACTION100
2.45-2.60.20871400.15692695X-RAY DIFFRACTION99.96
2.6-2.80.19511460.15592699X-RAY DIFFRACTION100
2.8-3.080.21751420.15012689X-RAY DIFFRACTION99.96
3.08-3.530.16131480.13462709X-RAY DIFFRACTION99.97
3.53-4.440.15251420.11652694X-RAY DIFFRACTION100
4.44-39.930.20431490.15522760X-RAY DIFFRACTION99.62

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