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Yorodumi- PDB-4mer: Crystal structure of the novel protein and virulence factor sHIP ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mer | ||||||
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Title | Crystal structure of the novel protein and virulence factor sHIP (Q99XU0) from Streptococcus pyogenes | ||||||
Components | streptococcal Histidine-rich glycoprotein Interacting Protein | ||||||
Keywords | UNKNOWN FUNCTION / helix / tetramer | ||||||
Function / homology | Protein of unknown function DUF4298 / Domain of unknown function (DUF4298) / identical protein binding / metal ion binding / DUF4298 domain-containing protein Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.41 Å | ||||||
Authors | Wisniewska, M. / Happonen, L. / Frick, M.-I. / Bjorck, L. / Streicher, W. / Malmstrom, J. / Wikstrom, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Functional and Structural Properties of a Novel Protein and Virulence Factor (Protein sHIP) in Streptococcus pyogenes. Authors: Wisniewska, M. / Happonen, L. / Kahn, F. / Varjosalo, M. / Malmstrom, L. / Rosenberger, G. / Karlsson, C. / Cazzamali, G. / Pozdnyakova, I. / Frick, I.M. / Bjorck, L. / Streicher, W. / ...Authors: Wisniewska, M. / Happonen, L. / Kahn, F. / Varjosalo, M. / Malmstrom, L. / Rosenberger, G. / Karlsson, C. / Cazzamali, G. / Pozdnyakova, I. / Frick, I.M. / Bjorck, L. / Streicher, W. / Malmstrom, J. / Wikstrom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mer.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mer.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 4mer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mer_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
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Full document | 4mer_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 4mer_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4mer_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/4mer ftp://data.pdbj.org/pub/pdb/validation_reports/me/4mer | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 11543.016 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: AP1 / Gene: M5005_Spy1730, SPy_2034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XU0 #2: 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: 2.9 Å3/Da / Density % sol: 57.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG3350, 0.2 M sodium malonate, 0.1 M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 8, 2012 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→50 Å / Num. all: 20497 / Num. obs: 20249 / % possible obs: 98 % |
Reflection shell | Resolution: 2.41→2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.41→48.63 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.514 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.387 / ESU R Free: 0.268 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.296 Å2
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Refinement step | Cycle: LAST / Resolution: 2.41→48.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.41→2.47 Å / Total num. of bins used: 20
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