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Yorodumi- PDB-2cnz: Salmonella enterica SafA pilin in complex with a 19-residue SafA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cnz | ||||||
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Title | Salmonella enterica SafA pilin in complex with a 19-residue SafA Nte peptide (V13A mutant) | ||||||
Components | (PUTATIVE OUTER MEMBRANE PROTEINVirulence-related outer membrane protein family) x 2 | ||||||
Keywords | FIBRIL PROTEIN / PILUS SUBUNIT / FOLD COMPLEMENTATION | ||||||
Function / homology | Function and homology information Saf-pilin pilus formation protein / Saf-pilin pilus formation protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | SALMONELLA TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cnz.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cnz.ent.gz | 30.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/2cnz ftp://data.pdbj.org/pub/pdb/validation_reports/cn/2cnz | HTTPS FTP |
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-Related structure data
Related structure data | 2cnyC 2co1C 2co2C 2co3C 2co4C 2co6C 2co7C C: citing same article (ref.) |
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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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Components on special symmetry positions |
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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/peptide | Mass: 2139.299 Da / Num. of mol.: 1 / Fragment: N-TERMINAL EXTENSION, RESIDUES 27-46 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) SALMONELLA TYPHIMURIUM (bacteria) / References: UniProt: Q8ZRK4 |
#3: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.65 % |
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Crystal grow | pH: 4.6 / Details: pH 4.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 45514 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAFA ANTE WT Resolution: 1.8→19.9 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.934 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN ATOMS FOR WHICH ELECTRON DENSITY IS MISSING ABOVE 1SIGMA WERE GIVEN A 0.01 OCCUPANCY
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.9 Å
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Refine LS restraints |
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