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Yorodumi- PDB-6sig: Epidermicin antimicrobial protein from Staphylococcus epidermidis -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sig | ||||||
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Title | Epidermicin antimicrobial protein from Staphylococcus epidermidis | ||||||
Components | Epidermicin locus structural protein | ||||||
Keywords | STRUCTURAL PROTEIN / antibiotic / helical | ||||||
Function / homology | Bacteriocin class II, aureocin-like / Aureocin-like type II bacteriocin / Epidermicin locus structural protein Function and homology information | ||||||
Biological species | Staphylococcus epidermidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Derrick, J.P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Iscience / Year: 2020 Title: Flowering Poration-A Synergistic Multi-Mode Antibacterial Mechanism by a Bacteriocin Fold. Authors: Hammond, K. / Lewis, H. / Halliwell, S. / Desriac, F. / Nardone, B. / Ravi, J. / Hoogenboom, B.W. / Upton, M. / Derrick, J.P. / Ryadnov, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sig.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sig.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 6sig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/6sig ftp://data.pdbj.org/pub/pdb/validation_reports/si/6sig | HTTPS FTP |
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-Related structure data
Related structure data | 6sifSC 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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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 6054.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Staphylococcus epidermidis (bacteria) / References: UniProt: H9BG66 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium Sulphate, 0.1M Sodium Acetate pH4.5, 28% PEG 2000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→49.78 Å / Num. obs: 42997 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 16.209 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.025 / Rrim(I) all: 0.065 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.58→1.62 Å / Rmerge(I) obs: 0.649 / Num. unique obs: 3140 / Rpim(I) all: 0.308 / Rrim(I) all: 0.781 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SIF Resolution: 1.58→49.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.203 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.76 Å2 / Biso mean: 23.404 Å2 / Biso min: 11 Å2
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Refinement step | Cycle: final / Resolution: 1.58→49.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.584→1.625 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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