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- PDB-7ec8: Polyethylene terephthalate hydrolyzing lipase PET2 mutant - F105R... -

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Basic information

Entry
Database: PDB / ID: 7ec8
TitlePolyethylene terephthalate hydrolyzing lipase PET2 mutant - F105R-E110K
ComponentsLipIAF5-2
KeywordsHYDROLASE / Polyethylene terephthalate hydrolase / lipase
Function / homologyCutinase / PET hydrolase-like / : / carboxylic ester hydrolase activity / Alpha/Beta hydrolase fold / LipIAF5-2
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNakamura, A.
CitationJournal: Acs Catalysis / Year: 2021
Title: Positive Charge Introduction on the Surface of Thermostabilized PET Hydrolase Facilitates PET Binding and Degradation.
Authors: Nakamura, A.
History
DepositionMar 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LipIAF5-2
B: LipIAF5-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,37819
Polymers63,2202
Non-polymers1,15717
Water11,800655
1
A: LipIAF5-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0177
Polymers31,6101
Non-polymers4066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LipIAF5-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,36112
Polymers31,6101
Non-polymers75111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.050, 72.490, 98.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein LipIAF5-2


Mass: 31610.246 Da / Num. of mol.: 2 / Mutation: F105R, E110K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: lipIAF5-2 / Plasmid: pET27b / Production host: Escherichia coli (E. coli) / References: UniProt: C3RYL0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / 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: 2 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M ammonium sulfate in 100 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.35→33.4 Å / Num. obs: 111811 / % possible obs: 99.5 % / Redundancy: 13.9 % / Biso Wilson estimate: 13.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.077 / Net I/σ(I): 23.9
Reflection shellResolution: 1.35→1.43 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 17635 / CC1/2: 0.772 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→33.4 Å / SU ML: 0.1685 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.3612 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1964 5588 5 %
Rwork0.1684 106188 -
obs0.1698 111776 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.56 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 71 655 4728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01164371
X-RAY DIFFRACTIONf_angle_d1.12065962
X-RAY DIFFRACTIONf_chiral_restr0.0943627
X-RAY DIFFRACTIONf_plane_restr0.0079787
X-RAY DIFFRACTIONf_dihedral_angle_d21.61481573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.360.42271740.40433303X-RAY DIFFRACTION94.3
1.36-1.380.31311830.31093477X-RAY DIFFRACTION98.79
1.38-1.40.3221840.29073488X-RAY DIFFRACTION98.55
1.4-1.410.33031830.27463483X-RAY DIFFRACTION99.48
1.41-1.430.30091830.25283480X-RAY DIFFRACTION98.89
1.43-1.450.24921850.23213510X-RAY DIFFRACTION98.77
1.45-1.470.22271840.21573497X-RAY DIFFRACTION99.62
1.47-1.490.22641840.20843494X-RAY DIFFRACTION99.24
1.49-1.520.23791850.2013501X-RAY DIFFRACTION99.25
1.52-1.540.23151830.1913493X-RAY DIFFRACTION99.51
1.54-1.570.23881860.19613524X-RAY DIFFRACTION99.81
1.57-1.60.20751840.1933498X-RAY DIFFRACTION99.51
1.6-1.630.22321850.18353538X-RAY DIFFRACTION99.65
1.63-1.660.2071870.18713546X-RAY DIFFRACTION99.68
1.66-1.70.22971850.17893515X-RAY DIFFRACTION99.78
1.7-1.740.18861860.17083519X-RAY DIFFRACTION99.81
1.74-1.780.21171880.17343572X-RAY DIFFRACTION99.95
1.78-1.830.19261840.16723513X-RAY DIFFRACTION99.89
1.83-1.880.21821870.1673563X-RAY DIFFRACTION99.97
1.88-1.940.20891860.16313523X-RAY DIFFRACTION100
1.94-2.010.20221880.15913584X-RAY DIFFRACTION99.97
2.01-2.090.19631870.16093550X-RAY DIFFRACTION100
2.09-2.190.18621880.16063562X-RAY DIFFRACTION100
2.19-2.30.19071880.15763586X-RAY DIFFRACTION99.97
2.3-2.450.16361880.14923570X-RAY DIFFRACTION100
2.45-2.640.18581890.15533588X-RAY DIFFRACTION100
2.64-2.90.17521910.1573624X-RAY DIFFRACTION100
2.9-3.320.17641900.15393612X-RAY DIFFRACTION100
3.32-4.180.16891930.13693672X-RAY DIFFRACTION100
4.18-33.40.16412000.15023803X-RAY DIFFRACTION99.65

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