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Yorodumi- PDB-3hr6: Structure of the Corynebacterium diphtheriae major pilin SpaA poi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hr6 | ||||||
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Title | Structure of the Corynebacterium diphtheriae major pilin SpaA points to a modular pilus assembly stabilizing isopeptide bonds | ||||||
Components | Putative surface-anchored fimbrial subunit | ||||||
Keywords | STRUCTURAL PROTEIN / CELL ADHESION / Multiple Ig-like domains / Cell wall / Peptidoglycan-anchor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Corynebacterium diphtheriae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Kang, H.J. / Paterson, N.G. / Gaspar, A.H. / Ton-That, H. / Baker, E.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: The Corynebacterium diphtheriae shaft pilin SpaA is built of tandem Ig-like modules with stabilizing isopeptide and disulfide bonds Authors: Kang, H.J. / Paterson, N.G. / Gaspar, A.H. / Ton-That, H. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hr6.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hr6.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hr6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/3hr6 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/3hr6 | 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: 46879.449 Da / Num. of mol.: 1 / Fragment: residues in UNP 53-486 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Gene: SpaA / Plasmid: pDest17 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q6NF81 |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-IOD / |
#4: 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: 2.34 Å3/Da / Density % sol: 47.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 3350, 0.1M NaF, 0.1M NaI, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.773 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2008 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.773 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. all: 58478 / Num. obs: 58478 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.69 Å / % possible all: 85.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0044 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 1.6→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.566 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.095 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.57 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.9078 Å / Origin y: 2.76 Å / Origin z: 39.9769 Å
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