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- PDB-8vek: IsPETase - ACC mutant -

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Basic information

Entry
Database: PDB / ID: 8vek
TitleIsPETase - ACC mutant
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PETase / protein engineering
Function / homology
Function and homology information


acetylesterase activity / poly(ethylene terephthalate) hydrolase / carboxylic ester hydrolase activity / xenobiotic catabolic process / extracellular region
Similarity search - Function
Dienelactone hydrolase / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesPiscinibacter sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsJoho, Y. / Royan, S. / Newton, S. / Caputo, A.T. / Ardevol Grau, A. / Jackson, C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Commonwealth Scientific and Industrial Research Organisation (CSIRO) Australia
CitationJournal: Chembiochem / Year: 2024
Title: Enhancing PET Degrading Enzymes: A Combinatory Approach.
Authors: Joho, Y. / Royan, S. / Caputo, A.T. / Newton, S. / Peat, T.S. / Newman, J. / Jackson, C. / Ardevol, A.
History
DepositionDec 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly(ethylene terephthalate) hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9515
Polymers28,5751
Non-polymers3764
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.764, 68.410, 79.298
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 Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 28574.795 Da / Num. of mol.: 1 / Mutation: D186A, N233C, S282C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piscinibacter sakaiensis (bacteria) / Gene: ISF6_4831 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.208 M ammonium sulfate, 23.2 w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.14→51.8 Å / Num. obs: 89827 / % possible obs: 90.9 % / Redundancy: 12.6 % / Biso Wilson estimate: 13.25 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.014 / Rrim(I) all: 0.05 / Net I/σ(I): 18.6
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 8.5 % / Rmerge(I) obs: 1.703 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8062 / CC1/2: 0.579 / Rpim(I) all: 0.601 / Rrim(I) all: 1.814 / % possible all: 57.1

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHENIX1.20.1_4487refinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→31.25 Å / SU ML: 0.0806 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1505 3857 4.92 %
Rwork0.1263 74605 -
obs0.1275 78462 76.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.41 Å2
Refinement stepCycle: LAST / Resolution: 1.14→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 22 328 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162150
X-RAY DIFFRACTIONf_angle_d1.43852964
X-RAY DIFFRACTIONf_chiral_restr0.1112328
X-RAY DIFFRACTIONf_plane_restr0.0157393
X-RAY DIFFRACTIONf_dihedral_angle_d13.3114793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.150.149610.232959X-RAY DIFFRACTION1.69
1.15-1.160.3319110.22173X-RAY DIFFRACTION5.21
1.16-1.180.1548210.2065336X-RAY DIFFRACTION10.01
1.18-1.20.1917240.2007492X-RAY DIFFRACTION14.36
1.2-1.210.1683340.1958720X-RAY DIFFRACTION20.83
1.21-1.230.2252490.17441041X-RAY DIFFRACTION30.35
1.23-1.250.2206790.17511504X-RAY DIFFRACTION43.61
1.25-1.270.221180.17072193X-RAY DIFFRACTION63.56
1.27-1.290.23881350.17052837X-RAY DIFFRACTION81.81
1.29-1.320.19581570.16523239X-RAY DIFFRACTION93.92
1.32-1.340.18441720.14983363X-RAY DIFFRACTION97.17
1.34-1.370.16471680.14433346X-RAY DIFFRACTION97.34
1.37-1.40.17711890.13063361X-RAY DIFFRACTION97.58
1.4-1.430.15521790.12753374X-RAY DIFFRACTION97.82
1.43-1.470.16461660.11743383X-RAY DIFFRACTION97.96
1.47-1.510.1411720.11233399X-RAY DIFFRACTION98
1.51-1.550.1292140.10453384X-RAY DIFFRACTION98.06
1.55-1.60.14221780.09853384X-RAY DIFFRACTION98.4
1.6-1.660.14151710.10213426X-RAY DIFFRACTION98.68
1.66-1.720.11951770.10823433X-RAY DIFFRACTION98.69
1.72-1.80.12932000.11693442X-RAY DIFFRACTION98.78
1.8-1.90.14811690.12033475X-RAY DIFFRACTION99.26
1.9-2.020.14981780.11723454X-RAY DIFFRACTION99.15
2.02-2.170.14241580.11673490X-RAY DIFFRACTION99.37
2.17-2.390.13241810.1193507X-RAY DIFFRACTION99.41
2.39-2.740.15751820.13023532X-RAY DIFFRACTION99.65
2.74-3.450.15711780.13483574X-RAY DIFFRACTION99.63
3.45-31.250.14811960.13083684X-RAY DIFFRACTION98.68

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