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Yorodumi- PDB-3qdp: Structural characterization of the interaction of colicin A, coli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qdp | ||||||
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Title | Structural characterization of the interaction of colicin A, colicin N, and TolB with TolAIII translocon | ||||||
Components | Protein tolA | ||||||
Keywords | PROTEIN TRANSPORT / TolA / Translocation / colicin / TolB / ColA / ColN / methylation | ||||||
Function / homology | Function and homology information cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell division site / disordered domain specific binding / cell cycle / symbiont entry into host cell ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / toxin transmembrane transporter activity / protein import / virion binding / cell division site / disordered domain specific binding / cell cycle / symbiont entry into host cell / cell division / protein domain specific binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Li, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural Evidence That Colicin A Protein Binds to a Novel Binding Site of TolA Protein in Escherichia coli Periplasm. Authors: Li, C. / Zhang, Y. / Vankemmelbeke, M. / Hecht, O. / Aleanizy, F.S. / Macdonald, C. / Moore, G.R. / James, R. / Penfold, C.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qdp.cif.gz | 28.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qdp.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/3qdp ftp://data.pdbj.org/pub/pdb/validation_reports/qd/3qdp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13180.879 Da / Num. of mol.: 1 / Fragment: TolA domain III, residues 302-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: tolA, cim, excC, lky, b0739, JW0729 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19934 | ||
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#2: Chemical | #3: 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: 2.91 Å3/Da / Density % sol: 57.75 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.28 Details: 0.2 M NaNO3, 2.2 M ammonium sulphate, pH 5.28, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97919 Å |
Detector | Type: PILATUS 6M / Detector: CCD / Date: Oct 29, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40.32 Å / Num. all: 8641 / Num. obs: 8641 / % possible obs: 100 % / Redundancy: 9.7 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.059 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 5 / Num. unique all: 1234 / Rsym value: 0.456 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→40.32 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 10.676 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.249 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→40.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / 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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