+Open data
-Basic information
Entry | Database: PDB / ID: 7m5i | ||||||
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Title | Endolysin from Escherichia coli O157:H7 phage FAHEc1 | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / Bacteriophage / peptidoglycan hydrolase / endolysin / enzyme / muramidase | ||||||
Function / homology | Function and homology information cytolysis / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Escherichia coli O157 typing phage 15 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Love, M.J. / Coombes, D. / Billington, C. / Dobson, R.C.J. | ||||||
Citation | Journal: Viruses / Year: 2021 Title: The Molecular Basis for Escherichia coli O157:H7 Phage FAHEc1 Endolysin Function and Protein Engineering to Increase Thermal Stability. Authors: Love, M.J. / Coombes, D. / Manners, S.H. / Abeysekera, G.S. / Billington, C. / Dobson, R.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7m5i.cif.gz | 144.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7m5i.ent.gz | 112.5 KB | Display | PDB format |
PDBx/mmJSON format | 7m5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/7m5i ftp://data.pdbj.org/pub/pdb/validation_reports/m5/7m5i | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: -3 - 153 / Label seq-ID: 3 - 159
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-Components
#1: Protein | Mass: 17939.588 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157 typing phage 15 (virus) Gene: rrrD, ECTP15_02508 / Variant: ERL 022447 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F6R9G3, lysozyme #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Sodium Chloride, 1.6 M Ammonium sulfate, 0.1 M Sodium HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→44.85 Å / Num. obs: 39675 / % possible obs: 99.9 % / Redundancy: 1 % / CC1/2: 0.999 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 1 % / Num. unique obs: 2064 / CC1/2: 0.575 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ET6A Resolution: 1.71→44.85 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.688 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.766 Å2
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Refinement step | Cycle: 1 / Resolution: 1.71→44.85 Å
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Refine LS restraints |
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