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Yorodumi- PDB-1o82: X-RAY STRUCTURE OF BACTERIOCIN AS-48 AT PH 4.5. SULPHATE BOUND FORM -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o82 | ||||||
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Title | X-RAY STRUCTURE OF BACTERIOCIN AS-48 AT PH 4.5. SULPHATE BOUND FORM | ||||||
Components | PEPTIDE ANTIBIOTIC AS-48 | ||||||
Keywords | PEPTIDE ANTIBIOTIC / BACTERIOCIN / CATIONIC ANTIBACTERIAL PEPTIDES / MEMBRANE PERMEABILIZATION / PROTEIN CRYSTALLOGRAPHY / CYCLIC POLYPEPTIDE / PROTEIN MEMBRANE INTERACTION | ||||||
Function / homology | Function and homology information killing of cells of another organism / defense response to bacterium / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.46 Å | ||||||
Authors | Sanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Martinez-Bueno, M. / Maqueda, M. / Cruz, V. / Albert, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structure of Bacteriocin as-48: From Soluble State to Membrane Bound State Authors: Sanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Valdivia, E. / Maqueda, M. / Cruz, V. / Albert, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o82.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o82.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 1o82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o82 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o82 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 7177.538 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: PEPTIDE LINK BETWEEN RESIDUES 1 AND 70 / Source: (natural) ENTEROCOCCUS FAECALIS (bacteria) / References: UniProt: Q47765 #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.42 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.5 Details: 0.2 M AMMONIUM SULFATE, 0.1 SODIUM ACETATE TRIHYDRATE PH 4.5, 12% W/V POLYETHYLENE GLYCOL 4000AS-48 10 MG/ML | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→25.25 Å / Num. obs: 54856 / % possible obs: 94.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 1.46 Å / Lowest resolution: 25.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 94.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 1.46→15 Å / SU B: 1.543 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.072 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
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Displacement parameters | Biso mean: 19.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→15 Å
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Refinement | *PLUS Lowest resolution: 15 Å / Rfactor Rfree: 0.2235 / Rfactor Rwork: 0.226 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.46 Å / Lowest resolution: 1.54 Å / Rfactor Rfree: 0.34 / Rfactor Rwork: 0.29 |