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Yorodumi- PDB-2x12: pH-induced modulation of Streptococcus parasanguinis adhesion by ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x12 | ||||||
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Title | pH-induced modulation of Streptococcus parasanguinis adhesion by Fap1 fimbriae | ||||||
Components | FIMBRIAE-ASSOCIATED PROTEIN FAP1 | ||||||
Keywords | CELL ADHESION / BIOFILM / CELL WALL / PEPTIDOGLYCAN-ANCHOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PARASANGUINIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å | ||||||
Authors | Ramboarina, S. / Murray, J.W. / Garnett, J. / Matthews, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Structural Insights Into Serine-Rich Fimbriae from Gram-Positive Bacteria. Authors: Ramboarina, S. / Garnett, J.A. / Zhou, M. / Li, Y. / Peng, Z. / Taylor, J.D. / Lee, W.-C. / Bodey, A. / Murray, J.W. / Alguel, Y. / Bergeron, J. / Bardiaux, B. / Sawyer, E. / Isaacson, R. / ...Authors: Ramboarina, S. / Garnett, J.A. / Zhou, M. / Li, Y. / Peng, Z. / Taylor, J.D. / Lee, W.-C. / Bodey, A. / Murray, J.W. / Alguel, Y. / Bergeron, J. / Bardiaux, B. / Sawyer, E. / Isaacson, R. / Tagliaferri, C. / Cota, E. / Nilges, M. / Simpson, P. / Ruiz, T. / Wu, H. / Matthews, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x12.cif.gz | 162.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x12.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 2x12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/2x12 ftp://data.pdbj.org/pub/pdb/validation_reports/x1/2x12 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.9818, 0.1886, -0.02117), Vector: |
-Components
#1: Protein | Mass: 37264.195 Da / Num. of mol.: 2 / Fragment: BETA DOMAIN, RESIDUES 174-505 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PARASANGUINIS (bacteria) / Strain: FW213 / Plasmid: PRSETA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: Q9ZFF9, UniProt: A1C3L3*PLUS |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.1 Å3/Da / Density % sol: 76 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: 0.1 M HEPES PH 8.0, 11% (W/V) PEG 6K, 10 MM SPERMINE-TETRA HCL HANGING DROP VAPOUR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.04 Å / Num. obs: 19567 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 7.58 % / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.19 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 7.88 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.61 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.9→38.405 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.888 / SU B: 26.334 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.42 / ESU R Free: 0.297 / 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 / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.212 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→38.405 Å
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Refine LS restraints |
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