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- PDB-3g69: 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: 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 | ||||||
![]() | 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 | ![]() | 102.1 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.4 KB | Display | ![]() |
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Full document | ![]() | 469.9 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3g66SC S: Starting model for refinement C: citing same article ( |
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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: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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