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- PDB-7sh6: Crystal structure of a PET hydrolase mutant from Ideonella Sakaiensis -

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Basic information

Entry
Database: PDB / ID: 7sh6
TitleCrystal structure of a PET hydrolase mutant from Ideonella Sakaiensis
ComponentsPoly(ethylene terephthalate) hydrolase
KeywordsHYDROLASE / PET hydrolase / PET degradation / Protein Engineering / Machine Learning
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 speciesIdeonella sakaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKim, W. / Zhang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125882 United States
CitationJournal: Nature / Year: 2022
Title: Machine learning-aided engineering of hydrolases for PET depolymerization.
Authors: Lu, H. / Diaz, D.J. / Czarnecki, N.J. / Zhu, C. / Kim, W. / Shroff, R. / Acosta, D.J. / Alexander, B.R. / Cole, H.O. / Zhang, Y. / Lynd, N.A. / Ellington, A.D. / Alper, H.S.
History
DepositionOct 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,9042
Polymers30,8071
Non-polymers961
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.942, 51.182, 84.047
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 / PET hydrolase / PETase / PET-digesting enzyme


Mass: 30807.482 Da / Num. of mol.: 1 / Mutation: S121E, D186H, R224Q, N233K, R280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ideonella sakaiensis (bacteria) / Strain: NBRC 110686 / TISTR 2288 / 201-F6 / Gene: ISF6_4831 / Production host: Pseudomonas putida KT2440 (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.: 362 / 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: 1.78 Å3/Da / Density % sol: 30.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M bis-TRIS pH 5.5, 2.0M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 40349 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Χ2: 1.127 / Net I/σ(I): 8.8 / Num. measured all: 267933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.44-1.463.50.19519010.9480.1130.2280.45194.3
1.46-1.494.20.1719210.9630.090.1940.41897
1.49-1.525.10.16119760.9740.0780.180.41498.9
1.52-1.556.60.15419880.9820.0650.1670.43899.9
1.55-1.587.30.14420250.9880.0570.1550.452100
1.58-1.627.40.12919650.9890.0510.1390.474100
1.62-1.667.40.12320150.9910.0480.1320.521100
1.66-1.717.30.11120280.9920.0440.120.557100
1.71-1.767.20.10320090.9930.0410.1110.61799.8
1.76-1.817.10.09119920.9940.0360.0980.64999.8
1.81-1.886.40.08620030.9940.0360.0930.736100
1.88-1.957.20.08220190.9950.0330.0880.905100
1.95-2.047.60.07420350.9960.0290.081.059100
2.04-2.157.50.07220080.9960.0280.0771.24999.9
2.15-2.297.30.06920360.9960.0270.0741.426100
2.29-2.467.10.06520360.9960.0260.071.59499.9
2.46-2.716.40.06120490.9970.0260.0671.83499.6
2.71-3.17.60.05920460.9970.0230.0632.149100
3.1-3.916.90.06121060.9960.0250.0662.78699.9
3.91-505.60.06621910.9920.0310.0733.09198.9

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.18rc3_3805refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IJ6

6ij6


Resolution: 1.44→43.71 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1678 1988 4.94 %
Rwork0.1577 38284 -
obs0.1583 40272 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.25 Å2 / Biso mean: 9.6769 Å2 / Biso min: 2.47 Å2
Refinement stepCycle: final / Resolution: 1.44→43.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 5 362 2282
Biso mean--17.01 22.72 -
Num. residues----261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062044
X-RAY DIFFRACTIONf_angle_d0.8652804
X-RAY DIFFRACTIONf_dihedral_angle_d6.029301
X-RAY DIFFRACTIONf_chiral_restr0.083306
X-RAY DIFFRACTIONf_plane_restr0.006373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.480.2181320.17162524265692
1.48-1.510.17881420.14692648279098
1.51-1.560.15041420.138227352877100
1.56-1.610.18261380.141227212859100
1.61-1.670.1681420.134327002842100
1.67-1.730.17471410.141727252866100
1.73-1.810.16571430.145327352878100
1.81-1.910.18671420.146727362878100
1.91-2.030.13831430.140727332876100
2.03-2.180.15871440.13827542898100
2.18-2.40.15771430.144227832926100
2.4-2.750.16181440.151827362880100
2.75-3.470.14471450.161128322977100
3.47-43.710.19741470.2122922306999

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