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- PDB-5xh3: Crystal structure of a novel PET hydrolase R103G/S131A mutant in ... -

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Basic information

Entry
Database: PDB / ID: 5xh3
TitleCrystal structure of a novel PET hydrolase R103G/S131A mutant in complex with HEMT from Ideonella sakaiensis 201-F6
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / Poly(ethylene terephthalate) hydrolase / substrate binding / 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 / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-856 / Poly(ethylene terephthalate) hydrolase
Similarity search - Component
Biological speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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 19, 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 1.3Nov 20, 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)27,7445
Polymers27,2351
Non-polymers5084
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.897, 51.282, 84.108
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: 27235.207 Da / Num. of mol.: 1 / 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-856 / O 4-(2-hydroxyethyl) O 1-methyl benzene-1,4-dicarboxylate


Mass: 224.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12O5
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.02 Å3/Da / Density % sol: 38.96 % / Mosaicity: 0.271 °
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: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 16, 2017
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.3→25 Å / Num. obs: 54696 / % possible obs: 99.6 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Χ2: 0.66 / Net I/σ(I): 9.8 / Num. measured all: 379525
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.3-1.355.90.3430.9390.1510.3760.36798.2
1.35-1.46.90.290.9630.1170.3130.38699.3
1.4-1.467.10.2140.980.0860.2310.41999.1
1.46-1.547.10.1570.9890.0630.1690.46399.6
1.54-1.647.10.1170.9930.0470.1270.54799.7
1.64-1.767.10.0870.9960.0350.0940.67699.8
1.76-1.947.10.060.9980.0240.0650.767100
1.94-2.227.10.0450.9990.0180.0490.962100
2.22-2.87.10.0370.9990.0150.041.08100
2.8-256.90.0320.9990.0130.0340.83299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4wfi


Resolution: 1.3→25 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.208 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.04
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1455 2691 4.9 %RANDOM
Rwork0.1176 ---
obs0.119 51930 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 103.72 Å2 / Biso mean: 13.677 Å2 / Biso min: 4.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20 Å2
2--0.25 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 1.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 32 244 2187
Biso mean--30.93 30.12 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022013
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9512751
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.675272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2923.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02215290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2061512
X-RAY DIFFRACTIONr_chiral_restr0.1260.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211561
X-RAY DIFFRACTIONr_rigid_bond_restr8.52432013
X-RAY DIFFRACTIONr_sphericity_free26.4775171
X-RAY DIFFRACTIONr_sphericity_bonded9.51152036
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 187 -
Rwork0.193 3707 -
all-3894 -
obs--97.42 %

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