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Yorodumi- PDB-7q4t: Structure of the Pseudomonas aeruginosa bacteriophage JG004 endol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7q4t | ||||||
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Title | Structure of the Pseudomonas aeruginosa bacteriophage JG004 endolysin Pae87 bound to a peptidoglycan fragment. | ||||||
Components |
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Keywords | HYDROLASE / endolysin / phage lysozyme / muramidase / monomodular / antimicrobial. | ||||||
Function / homology | N-acetylmuramidase / N-acetylmuramidase / Lysozyme-like domain superfamily / DI(HYDROXYETHYL)ETHER / Endolysin Function and homology information | ||||||
Biological species | Pseudomonas phage JG004 (virus) Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Seoane-Blanco, M. / van Raaij, M.J. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain. Authors: Vazquez, R. / Seoane-Blanco, M. / Rivero-Buceta, V. / Ruiz, S. / van Raaij, M.J. / Garcia, P. #1: Journal: Front Microbiol / Year: 2021 Title: Mining of Gram-Negative Surface-Active Enzybiotic Candidates by Sequence-Based Calculation of Physicochemical Properties. Authors: Vazquez, R. / Blanco-Ganan, S. / Ruiz, S. / Garcia, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7q4t.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7q4t.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7q4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/7q4t ftp://data.pdbj.org/pub/pdb/validation_reports/q4/7q4t | HTTPS FTP |
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-Related structure data
Related structure data | 7q4sSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AAALbL
#1: Protein | Mass: 23084.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage JG004 (virus) / Gene: PJG4_087 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F4YDQ3 |
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#2: Protein/peptide | Mass: 218.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa PAO1 (bacteria) |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acid Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 132 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 Å3/Da / Density % sol: 38.7 % / Description: bar-shaped |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.12 M Tris-HCl, 20% (w/v) PEG 5000 MME, 8% (v/v) ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97933 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→69.21 Å / Num. obs: 49510 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.938 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 6 % / Rmerge(I) obs: 0.753 / Mean I/σ(I) obs: 2 / Num. unique obs: 2412 / CC1/2: 0.903 / Rpim(I) all: 0.33 / Rrim(I) all: 0.825 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7Q4S Resolution: 1.27→45.854 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.72 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.04 / ESU R Free: 0.04 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.016 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→45.854 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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