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- PDB-3g66: The crystal structure of Streptococcus pneumoniae Sortase C provi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3g66 | ||||||
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Title | The crystal structure of Streptococcus pneumoniae Sortase C provides novel insights into catalysis as well as pilin substrate specificity | ||||||
![]() | Sortase C | ||||||
![]() | TRANSFERASE / Sortase / Pilus / S. pneumoniae | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Neiers, F. / Madhurantakam, C. / Falker, S. / Manzano, C. / Dessen, A. / Normark, S. / Henriques-Normark, B. / Achour, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.9 KB | Display | ![]() |
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PDB format | ![]() | 77.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.6 KB | Display | ![]() |
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Full document | ![]() | 459.4 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g69C ![]() 2w1jS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6 M magnesium sulfate, 0.1 M MES pH 6.5., VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.7→42.02 Å / Num. obs: 52404 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7580 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2W1J Resolution: 1.7→32.29 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.057 / SU ML: 0.07 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.111 / 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: 23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→32.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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