+Open data
-Basic information
Entry | Database: PDB / ID: 3toc | ||||||
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Title | Crystal structure of Streptococcus pyogenes Csn2 | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.201 Å | ||||||
Authors | Bae, E. / Jung, D.K. / Koo, Y. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal Structure of Streptococcus pyogenes Csn2 Reveals Calcium-Dependent Conformational Changes in Its Tertiary and Quaternary Structure Authors: Koo, Y. / Jung, D.K. / Bae, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3toc.cif.gz | 180.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3toc.ent.gz | 152.9 KB | Display | PDB format |
PDBx/mmJSON format | 3toc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/3toc ftp://data.pdbj.org/pub/pdb/validation_reports/to/3toc | HTTPS FTP |
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-Related 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: 26235.541 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: serotype M1 / Gene: M5005_Spy0772, SPy_1049 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99ZV9 #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: 3.47 Å3/Da / Density % sol: 64.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.3M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97910, 0.97927, 0.96404 | ||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 2, 2011 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→50 Å / Num. obs: 36996 / % possible obs: 98.7 % / Biso Wilson estimate: 44.44 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.201→29.173 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.7764 / SU ML: 0.36 / σ(F): 2.14 / Phase error: 28.75 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.368 Å2 / ksol: 0.334 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.59 Å2 / Biso mean: 59.9489 Å2 / Biso min: 25.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.201→29.173 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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