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Yorodumi- PDB-1o84: Crystal Structure of Bacteriocin AS-48. N-decyl-beta-D-maltoside ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1o84 | |||||||||
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Title | Crystal Structure of Bacteriocin AS-48. N-decyl-beta-D-maltoside Bound. | |||||||||
Components | PEPTIDE ANTIBIOTIC AS-48 | |||||||||
Keywords | PEPTIDE ANTIBIOTIC / BACTERIOCIN / ANTIBACTERIAL PEPTIDE / 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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Sanchez-Barrena, M.J. / Martinez-Ripoll, M. / Galvez, A. / Valdivia, E. / 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 | 1o84.cif.gz | 39.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o84.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 1o84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o84_validation.pdf.gz | 824.9 KB | Display | wwPDB validaton report |
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Full document | 1o84_full_validation.pdf.gz | 828.2 KB | Display | |
Data in XML | 1o84_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1o84_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o8/1o84 ftp://data.pdbj.org/pub/pdb/validation_reports/o8/1o84 | HTTPS FTP |
-Related structure data
-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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.6455, 0.1237, 0.7537), Vector: |
-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 7177.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CYCLIC PROTEIN, LINK BETWEEN M1 AND W70 / Source: (natural) ENTEROCOCCUS FAECALIS (bacteria) / References: UniProt: Q47765 #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | |
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-Non-polymers , 4 types, 32 molecules
#3: Chemical | ChemComp-GOL / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-D10 / | #6: 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: 2.69 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7.5 Details: CRYSTALS WERE GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING AS48 (20 MG/ML), 18 MM N-DECYL-BETA-D-MALTOSIDE AND RESERVOIR SOLUTION (0.2 M AMMONIUM SULPHATE,25 % W/V ...Details: CRYSTALS WERE GROWN USING VAPOUR DIFFUSION TECHNIQUES FROM DROPS CONTAINING AS48 (20 MG/ML), 18 MM N-DECYL-BETA-D-MALTOSIDE AND RESERVOIR SOLUTION (0.2 M AMMONIUM SULPHATE,25 % W/V POLYETHYLENE GLYCOL 4000) IN A RATIO 4:1:5, pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ROTATING ANODE / Type: ENRAF NONIUS / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→34.3 Å / Num. obs: 4544 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 34.3 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.138 |
Reflection shell | *PLUS % possible obs: 100 % / Redundancy: 9 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→10 Å / SU B: 15.606 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Details: NCS RESTRAINTS USED
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Displacement parameters | Biso mean: 44.965 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refinement | *PLUS Highest resolution: 2.8 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.236 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.85 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.286 |