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Yorodumi- PDB-3g69: The crystal structure of Streptococcus pneumoniae Sortase C provi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g69 | ||||||
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Title | The crystal structure of Streptococcus pneumoniae Sortase C provides novel insights into catalysis as well as pilin substrate specificity | ||||||
Components | Sortase C | ||||||
Keywords | TRANSFERASE / Sortase / Pilus / S. pneumoniae | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Neiers, F. / Madhurantakam, C. / Falker, S. / Manzano, C. / Dessen, A. / Normark, S. / Henriques-Normark, B. / Achour, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Two crystal structures of pneumococcal pilus sortase C provide novel insights into catalysis and substrate specificity. Authors: Neiers, F. / Madhurantakam, C. / Falker, S. / Manzano, C. / Dessen, A. / Normark, S. / Henriques-Normark, B. / Achour, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g69.cif.gz | 102.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g69.ent.gz | 76.4 KB | Display | PDB format |
PDBx/mmJSON format | 3g69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g69_validation.pdf.gz | 462.4 KB | Display | wwPDB validaton report |
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Full document | 3g69_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 3g69_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 3g69_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/3g69 ftp://data.pdbj.org/pub/pdb/validation_reports/g6/3g69 | HTTPS FTP |
-Related structure data
Related structure data | 3g66SC S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24042.291 Da / Num. of mol.: 2 / Fragment: UNP residues 47-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0467, srtC / Plasmid: pET24c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A7KT63 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.59 Å3/Da / Density % sol: 52.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M MES pH 7.0 and 1.9 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 21, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→49.39 Å / Num. obs: 31946 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.011 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 6.3 / Num. unique all: 4490 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G66 Resolution: 2→43.6 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 4.445 / SU ML: 0.126 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.181 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.036 Å2
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Refinement step | Cycle: LAST / Resolution: 2→43.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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