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- PDB-8vem: IsPETase - ACCE mutant -

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Basic information

Entry
Database: PDB / ID: 8vem
TitleIsPETase - ACCE 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: 1.711 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 1.1Nov 13, 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)28,7132
Polymers28,6171
Non-polymers961
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.778, 59.085, 78.602
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PET hydrolase / PETase / PET-digesting enzyme


Mass: 28616.830 Da / Num. of mol.: 1 / Mutation: S136E, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.138 M ammonium sulfate, 30 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: MX1 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.711→47.229 Å / Num. obs: 16551 / % possible obs: 93 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.047 / Rrim(I) all: 0.173 / Net I/σ(I): 11.6
Reflection shellResolution: 1.711→1.858 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.916 / Num. unique obs: 829 / CC1/2: 0.53 / Rpim(I) all: 0.574 / Rrim(I) all: 2.003 / % possible all: 54.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.711→47.23 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU R Cruickshank DPI: 1.712 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.187 / SU Rfree Cruickshank DPI: 0.181
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 785 -RANDOM
Rwork0.2119 ---
obs0.2136 16551 63.2 %-
Displacement parametersBiso mean: 31.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.7545 Å20 Å20 Å2
2--5.4342 Å20 Å2
3----2.6797 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.711→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 5 181 2108
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083984HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.027183HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1215SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes668HARMONIC5
X-RAY DIFFRACTIONt_it2047HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion285SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3773SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.47
X-RAY DIFFRACTIONt_other_torsion14.22
LS refinement shellResolution: 1.711→1.82 Å
RfactorNum. reflection% reflection
Rfree0.2362 20 -
Rwork0.3059 --
obs--9.54 %
Refinement TLS params.Origin x: -6.7743 Å / Origin y: 1.8124 Å / Origin z: -5.7475 Å
111213212223313233
T-0.1012 Å20.0287 Å20.0243 Å2-0.0823 Å20.0219 Å2---0.1353 Å2
L1.7658 °20.3547 °21.1744 °2-0.9955 °20.2386 °2--3.96 °2
S-0.0049 Å °-0.0771 Å °0.4333 Å °-0.0771 Å °0.0554 Å °0.5148 Å °0.4333 Å °0.5148 Å °-0.0505 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 290
2X-RAY DIFFRACTION1{ A|* }A301

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