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- PDB-5xfz: Crystal structure of a novel PET hydrolase R103G/S131A mutant fro... -

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Basic information

Entry
Database: PDB / ID: 5xfz
TitleCrystal structure of a novel PET hydrolase R103G/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 / Resolution: 1.55 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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)28,0278
Polymers27,3661
Non-polymers6617
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.945, 51.618, 84.590
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27366.400 Da / Num. of mol.: 1 / Fragment: UNP residues 30-290 / Mutation: R103G, 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.03 Å3/Da / Density % sol: 39.47 % / Mosaicity: 0.465 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium Sulfate, NaCl, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2017
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 33154 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.039 / Rrim(I) all: 0.086 / Χ2: 0.85 / Net I/σ(I): 7.7 / Num. measured all: 157183
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.614.60.4910.8590.2550.5550.70399.9
1.61-1.674.80.4120.890.2080.4630.7100
1.67-1.754.80.3150.930.1580.3540.747100
1.75-1.844.80.2370.9590.1190.2660.811100
1.84-1.954.80.1630.980.0820.1830.815100
1.95-2.14.80.1090.990.0550.1220.888100
2.1-2.314.80.0780.9950.0390.0870.866100
2.31-2.654.80.0680.9960.0340.0761.046100
2.65-3.344.70.0610.9960.0310.0681.08199.6
3.34-254.60.0310.9990.0160.0350.83399.5

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Processing

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

4wfi


Resolution: 1.55→25 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.343 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1695 1637 5 %RANDOM
Rwork0.1385 ---
obs0.1401 31429 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.92 Å2 / Biso mean: 13.725 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 1.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1919 0 38 235 2192
Biso mean--42.62 26.11 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022017
X-RAY DIFFRACTIONr_bond_other_d00.021764
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9492751
X-RAY DIFFRACTIONr_angle_other_deg0.83834107
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92123.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78815288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2751512
X-RAY DIFFRACTIONr_chiral_restr0.1120.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02411
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 118 -
Rwork0.208 2278 -
all-2396 -
obs--99.92 %

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