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- PDB-7ecb: Polyethylene terephthalate hydrolyzing lipase PET2 mutant - R47C-... -

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Basic information

Entry
Database: PDB / ID: 7ecb
TitlePolyethylene terephthalate hydrolyzing lipase PET2 mutant - R47C-G89C-F105R-E110K-S156P-G180A-T297P
ComponentsLipIAF5-2
KeywordsHYDROLASE / Polyethylene terephthalate hydrolase / lipase
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold / hydrolase activity / LipIAF5-2
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 12, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 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: LipIAF5-2


Theoretical massNumber of molelcules
Total (without water)31,6221
Polymers31,6221
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.240, 86.720, 46.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

21A-675-

HOH

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Components

#1: Protein LipIAF5-2


Mass: 31622.363 Da / Num. of mol.: 1 / Mutation: R47C, G89C, F105R, E110K, S156P, G180A, T297P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: lipIAF5-2 / Production host: Escherichia coli (E. coli) / References: UniProt: C3RYL0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10% PEG3350 in 100 mM Tris-HCl pH 7.5

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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: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.83→38.08 Å / Num. obs: 24351 / % possible obs: 99.84 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Net I/σ(I): 13.1
Reflection shellResolution: 1.83→1.94 Å / Redundancy: 7 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 3 / Num. unique obs: 3841 / CC1/2: 0.851 / % possible all: 99.13

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EC8

7ec8


Resolution: 1.83→38.08 Å / SU ML: 0.1809 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.9402 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1925 1217 5 %
Rwork0.1499 23129 -
obs0.152 24346 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.84 Å2
Refinement stepCycle: LAST / Resolution: 1.83→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 0 286 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01642056
X-RAY DIFFRACTIONf_angle_d1.24422811
X-RAY DIFFRACTIONf_chiral_restr0.0825302
X-RAY DIFFRACTIONf_plane_restr0.0083369
X-RAY DIFFRACTIONf_dihedral_angle_d6.16211201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.910.25391310.21472493X-RAY DIFFRACTION98.42
1.91-1.990.21561340.18452531X-RAY DIFFRACTION99.93
1.99-2.10.21561340.16322550X-RAY DIFFRACTION99.96
2.1-2.230.24251320.16282522X-RAY DIFFRACTION99.96
2.23-2.40.22851340.15122558X-RAY DIFFRACTION99.93
2.4-2.640.20321350.1572558X-RAY DIFFRACTION99.93
2.64-3.030.17371350.14842576X-RAY DIFFRACTION100
3.03-3.810.17441370.13532602X-RAY DIFFRACTION100
3.81-38.080.15191450.12762739X-RAY DIFFRACTION99.9

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