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Yorodumi- PDB-2co6: Salmonella enterica SafA pilin in complex with the SafB chaperone... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2co6 | ||||||
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Title | Salmonella enterica SafA pilin in complex with the SafB chaperone (Type I) | ||||||
Components |
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Keywords | FIBRIL PROTEIN / PILUS SUBUNIT / ADHESION / STRAND COMPLEMENTATION / PATHOGENESIS / CHAPERONE | ||||||
Function / homology | Function and homology information chaperone-mediated protein folding / cell wall organization / outer membrane-bounded periplasmic space Similarity search - Function | ||||||
Biological species | SALMONELLA TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Remaut, H. / Rose, R.J. / Hannan, T.J. / Hultgren, S.J. / Radford, S.E. / Ashcroft, A.E. / Waksman, G. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Donor-Strand Exchange in Chaperone-Assisted Pilus Assembly Proceeds Through a Concerted Beta-Strand Displacement Mechanism Authors: Remaut, H. / Rose, R.J. / Hannan, T.J. / Hultgren, S.J. / Radford, S.E. / Ashcroft, A.E. / Waksman, G. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2co6.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2co6.ent.gz | 60.1 KB | Display | PDB format |
PDBx/mmJSON format | 2co6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/2co6 ftp://data.pdbj.org/pub/pdb/validation_reports/co/2co6 | HTTPS FTP |
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-Related structure data
Related structure data | 2cnyC 2cnzC 2co1C 2co2C 2co3C 2co4C 2co7C 1l4iS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350THE N-TERMINAL EXTENSION PEPTIDE OF ONE SUBUNIT, CHAIN B,INSERTS INTO THE FOLD OF ANOTHER, CHAIN A. THIS INTERACTIONIS REPETED IN THE POLYMER, AN N-TERMINAL EXTENSION OFMOLECULE C WOULD INSERT IN TO THE SUBUNIT OF MOLECULE B , DINTO C ETC |
-Components
#1: Protein | Mass: 13136.663 Da / Num. of mol.: 1 / Fragment: CORE PILIN DOMAIN, NTE DELETED, RESIDUES 48-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK4 |
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#2: Protein | Mass: 24023.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q8ZRK3 |
#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: 1.94 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | pH: 8.5 Details: 30% PEG 4000, 100 MM TRIS-HCL PH8.5, 200 MM SODIUM ACETATE, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.0726 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0726 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 20162 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1L4I Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.822 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.58 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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