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Yorodumi- PDB-5leo: Complex structure of lysostaphin SH3b domain with peptidoglycan f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5leo | ||||||
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Title | Complex structure of lysostaphin SH3b domain with peptidoglycan fragment | ||||||
Components |
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Keywords | CELL ADHESION / lysostaphin / peptidoglycan / complex / cell wall targeting/binding domain / SH3 | ||||||
Function / homology | Function and homology information lysostaphin / septum digestion after cytokinesis / cell division site / cell outer membrane / cell wall organization / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Staphylococcaceae (Staphylococcus group) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Jagielska, E. / Nowak, E. / Bochtler, M. / Sabala, I. | ||||||
Funding support | Poland, 1items
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Citation | Journal: To Be Published Title: Complex structure of lysostaphin SH3doamin with peptidoglycan fragment Authors: Jagielska, E. / Nowak, E. / Bochtler, M. / Sabala, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5leo.cif.gz | 100.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5leo.ent.gz | 77.3 KB | Display | PDB format |
PDBx/mmJSON format | 5leo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5leo_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 5leo_full_validation.pdf.gz | 456.1 KB | Display | |
Data in XML | 5leo_validation.xml.gz | 13 KB | Display | |
Data in CIF | 5leo_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/5leo ftp://data.pdbj.org/pub/pdb/validation_reports/le/5leo | HTTPS FTP |
-Related structure data
Related structure data | 4lxcS S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 10570.948 Da / Num. of mol.: 2 / Fragment: SH3b domain, UNP Residues 401-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcaceae (Staphylococcus group) Gene: lss / Production host: Escherichia coli (E. coli) / References: UniProt: P10547, lysostaphin #2: Protein/peptide | Mass: 303.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcaceae (Staphylococcus group) #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 1.99 Å3/Da / Density % sol: 38.21 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Buffer system 3 (0.1 M Tris (base), Bicine buffer, pH 8.5), 0.09 M NPS (NaNO3, Na2HPO4, (NH4)SO4), 37.5% MPD (racemic), PEG 1000, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→60 Å / Num. obs: 25084 / % possible obs: 98.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 5.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LXC Resolution: 1.6→39.402 Å / SU ML: 0.2 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 22.79
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→39.402 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -27.8405 Å / Origin y: 4.0045 Å / Origin z: 82.5817 Å
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Refinement TLS group | Selection details: all |