+Open data
-Basic information
Entry | Database: PDB / ID: 1a87 | ||||||
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Title | COLICIN N | ||||||
Components | COLICIN N | ||||||
Keywords | BACTERIOCIN / TOXIN / PORE-FORMING ACTIVITY | ||||||
Function / homology | Function and homology information negative regulation of ion transmembrane transporter activity / pore-forming activity / killing of cells of another organism / defense response to Gram-negative bacterium / transmembrane transporter binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å | ||||||
Authors | Vetter, I.R. / Parker, M.W. / Tucker, A.D. / Lakey, J.H. / Pattus, F. / Tsernoglou, D. | ||||||
Citation | Journal: Structure / Year: 1998 Title: Crystal structure of a colicin N fragment suggests a model for toxicity. Authors: Vetter, I.R. / Parker, M.W. / Tucker, A.D. / Lakey, J.H. / Pattus, F. / Tsernoglou, D. #1: Journal: Protein Toxin Structure / Year: 1996 Title: Insights Into Membrane Insertion Based on Studies of Colicins Authors: Vetter, I.R. / Parker, M.W. / Pattus, F. / Tsernoglou, D. #2: Journal: Eur.J.Biochem. / Year: 1993 Title: Characterization of the Receptor and Translocator Domains of Colicin N Authors: El Kouhen, R. / Fierobe, H.P. / Scianimanico, S. / Steiert, M. / Pattus, F. / Pages, J.M. #3: Journal: Eur.Biophys.J. / Year: 1990 Title: Colicin N Forms Voltage-and Ph-Dependent Channels in Planar Lipid Bilayer Membranes Authors: Wilmsen, H.U. / Pugsley, A.P. / Pattus, F. #4: Journal: Mol.Microbiol. / Year: 1990 Title: Involvement of Ompf During Reception and Translocation Steps of Colicin N Entry Authors: Bourdineaud, J.P. / Fierobe, H.P. / Lazdunski, C. / Pages, J.M. #5: Journal: Mol.Microbiol. / Year: 1987 Title: Nucleotide Sequencing of the Structural Gene for Colicin N Reveals Homology between the Catalytic, C-Terminal Domains of Colicins a and N Authors: Pugsley, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a87.cif.gz | 70.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a87.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/1a87 ftp://data.pdbj.org/pub/pdb/validation_reports/a8/1a87 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35146.270 Da / Num. of mol.: 1 / Fragment: RECEPTOR-BINDING AND PORE-FORMING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Variant: BZB 1019 / Plasmid: PCHAP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P08083 |
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#2: 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: 4.17 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 7 / PH range high: 5.6 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→22.7 Å / Num. obs: 10644 / % possible obs: 93.5 % / Biso Wilson estimate: 57.5 Å2 / Rsym value: 0.083 / Net I/σ(I): 33.07 |
Reflection shell | Resolution: 3.1→3.2 Å / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3.1→23 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: POSTERIORI / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Bsol: 300 Å2 / ksol: 0.8 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→23 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5EB / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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