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- PDB-5xfy: Crystal structure of a novel PET hydrolase S131A mutant from Ideo... -

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Basic information

Entry
Database: PDB / ID: 5xfy
TitleCrystal structure of a novel PET hydrolase S131A mutant from Ideonella sakaiensis 201-F6
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase / inhibitor
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 family / Cutinase / PET hydrolase-like / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsHan, X. / Liu, W.D. / Zheng, Y.Y. / Chen, C.C. / Guo, R.T.
CitationJournal: Nat Commun / Year: 2017
Title: Structural insight into catalytic mechanism of PET hydrolase
Authors: Han, X. / Liu, W. / Huang, J.W. / Ma, J. / Zheng, Y. / Ko, T.P. / Xu, L. / Cheng, Y.S. / Chen, C.C. / Guo, R.T.
History
DepositionApr 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 22, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)27,7165
Polymers27,3351
Non-polymers3804
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-15 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.185, 50.331, 40.979
Angle α, β, γ (deg.)90.000, 92.240, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Poly(ethylene terephthalate) hydrolase / PETase


Mass: 27335.348 Da / Num. of mol.: 1 / Fragment: UNP residues 30-290 / Mutation: S131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (strain 201-F6) (bacteria)
Strain: 201-F6 / Gene: ISF6_4831 / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0K8P6T7, poly(ethylene terephthalate) hydrolase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.85 % / Mosaicity: 0.733 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium Sulfate, NaCl, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 27, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→25 Å / Num. obs: 45597 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.016 / Rrim(I) all: 0.04 / Χ2: 1.808 / Net I/σ(I): 24.9 / Num. measured all: 261939
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.455.80.20745620.9770.0940.2281.392100
1.45-1.515.80.15545700.9870.070.171.439100
1.51-1.585.80.11945470.9920.0540.1311.508100
1.58-1.665.80.09545290.9950.0430.1051.597100
1.66-1.765.70.07845470.9960.0350.0861.873100
1.76-1.95.70.0645550.9970.0270.0662.04100
1.9-2.095.80.04245930.9990.0190.0461.907100
2.09-2.395.60.03845540.9990.0170.0422.278100
2.39-3.015.90.03345900.9990.0150.0372.219100
3.013-255.60.02745500.9990.0130.031.84297.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WFI

4wfi


Resolution: 1.4→25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.716 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1589 2306 5.1 %RANDOM
Rwork0.1344 ---
obs0.1355 43291 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.7 Å2 / Biso mean: 16.788 Å2 / Biso min: 8 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.32 Å2
2--0.68 Å2-0 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 1.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1918 0 21 190 2129
Biso mean--37.26 30.07 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191999
X-RAY DIFFRACTIONr_bond_other_d0.0010.021751
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9452732
X-RAY DIFFRACTIONr_angle_other_deg0.77834080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03323.50677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52515289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1521513
X-RAY DIFFRACTIONr_chiral_restr0.1020.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212283
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02410
LS refinement shellResolution: 1.401→1.437 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.177 162 -
Rwork0.156 3192 -
all-3354 -
obs--99.08 %

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