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Yorodumi- PDB-2x9x: STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x9x | ||||||
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Title | STRUCTURE OF THE PILUS BACKBONE (RRGB) FROM STREPTOCOCCUS PNEUMONIAE | ||||||
Components | CELL WALL SURFACE ANCHOR FAMILY PROTEIN | ||||||
Keywords | CELL ADHESION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. ...Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. / Rappuoli, R. / Lesley, S. / Covacci, A. / Masignani, V. / Ferlenghi, I. | ||||||
Citation | Journal: Plos One / Year: 2010 Title: Supramolecular Organization of the Repetitive Backbone Unit of the Streptococcus Pneumoniae Pilus. Authors: Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. / Rappuoli, R. / Lesley, S. / Covacci, A. / ...Authors: Spraggon, G. / Koesema, E. / Scarselli, M. / Malito, E. / Biagini, M. / Norais, N. / Emolo, C. / Barocchi, M.A. / Giusti, F. / Hilleringmann, M. / Rappuoli, R. / Lesley, S. / Covacci, A. / Masignani, V. / Ferlenghi, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9x.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9x.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9x ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9x | HTTPS FTP |
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-Related structure data
Related structure data | 2x9wSC 2x9yC 2x9zC 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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-Components
#1: Protein | Mass: 48210.090 Da / Num. of mol.: 1 / Fragment: BACKBONE SUBUNIT PILI, RESIDUES 184-627 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ISOPEPTIDE-BOND LINKS N318 AND K193, N428 AND K349, N623 AND K453 Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: SPEEDET / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q97SC2, UniProt: A0A0H2UNM7*PLUS |
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#2: Chemical | ChemComp-IMD / |
#3: Chemical | ChemComp-NA / |
#4: 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: 2.72 Å3/Da / Density % sol: 54.7 % / Description: NONE |
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Crystal grow | Details: PROTEIN WAS CRYSTALLIZED FROM 0.05 POTASSIUM DIHYDROGEN PHOSPHATE, 20% PEG-8000 PH 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 85582 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 16.74 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.3 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X9W Resolution: 1.5→46.665 Å / SU ML: 0.23 / σ(F): 1.33 / Phase error: 19.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.133 Å2 / ksol: 0.379 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→46.665 Å
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Refine LS restraints |
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LS refinement shell |
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