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Yorodumi- PDB-8q2g: X-ray structure of LysECD7 endolysin against Gram-negative bacteria -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q2g | ||||||
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Title | X-ray structure of LysECD7 endolysin against Gram-negative bacteria | ||||||
Components | Peptidoglycan L-alanyl-D-glutamate endopeptidase | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Endolysins / Bacteriophage lytic enzymes / Gram-negative bacteria / Antibacterial therapy / Antimicrobial agents / ANTIBIOTIC | ||||||
Function / homology | Peptidase M15C / D-alanyl-D-alanine carboxypeptidase / Hedgehog signalling/DD-peptidase zinc-binding domain superfamily / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / Peptidoglycan L-alanyl-D-glutamate endopeptidase Function and homology information | ||||||
Biological species | Escherichia phage ECD7 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Prudnikova, T. / Grinkevich, P. / Vasina, D.V. | ||||||
Funding support | 1items
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Citation | Journal: J.Biomed.Sci. / Year: 2024 Title: Development of novel antimicrobials with engineered endolysin LysECD7-SMAP to combat Gram-negative bacterial infections. Authors: Vasina, D.V. / Antonova, N.P. / Gushchin, V.A. / Aleshkin, A.V. / Fursov, M.V. / Fursova, A.D. / Gancheva, P.G. / Grigoriev, I.V. / Grinkevich, P. / Kondratev, A.V. / Kostarnoy, A.V. / ...Authors: Vasina, D.V. / Antonova, N.P. / Gushchin, V.A. / Aleshkin, A.V. / Fursov, M.V. / Fursova, A.D. / Gancheva, P.G. / Grigoriev, I.V. / Grinkevich, P. / Kondratev, A.V. / Kostarnoy, A.V. / Lendel, A.M. / Makarov, V.V. / Nikiforova, M.A. / Pochtovyi, A.A. / Prudnikova, T. / Remizov, T.A. / Shevlyagina, N.V. / Siniavin, A.E. / Smirnova, N.S. / Terechov, A.A. / Tkachuk, A.P. / Usachev, E.V. / Vorobev, A.M. / Yakimakha, V.S. / Yudin, S.M. / Zackharova, A.A. / Zhukhovitsky, V.G. / Logunov, D.Y. / Gintsburg, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q2g.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q2g.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 8q2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q2g_validation.pdf.gz | 420 KB | Display | wwPDB validaton report |
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Full document | 8q2g_full_validation.pdf.gz | 423.7 KB | Display | |
Data in XML | 8q2g_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | 8q2g_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/8q2g ftp://data.pdbj.org/pub/pdb/validation_reports/q2/8q2g | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16117.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage ECD7 (virus) / Gene: cwlK / Plasmid: pET42b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A220NTE5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.54 Å3/Da / Density % sol: 65.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M Ammonium sulfate, 20% w/v Polyethylene glycol 3,350 pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→42.174 Å / Num. obs: 10864 / % possible obs: 97.4 % / Redundancy: 6 % / CC1/2: 0.99 / Net I/σ(I): 13.04 |
Reflection shell | Resolution: 2.49→2.56 Å / Num. unique obs: 3326 / CC1/2: 0.81 / % possible all: 93.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→42.174 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.845 / WRfactor Rfree: 0.337 / WRfactor Rwork: 0.263 / SU B: 18.5 / SU ML: 0.384 / Average fsc free: 0.6957 / Average fsc work: 0.7566 / Cross valid method: FREE R-VALUE / ESU R: 0.497 / ESU R Free: 0.383 / Details: Hydrogens have not been used
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.967 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→42.174 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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