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Yorodumi- PDB-3t46: Crystal structure of Staphylococcal Complement Inhibitor D (SCIN-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t46 | ||||||
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Title | Crystal structure of Staphylococcal Complement Inhibitor D (SCIN-D) at 1.5 Angstrom | ||||||
Components | SCIN-D | ||||||
Keywords | IMMUNE SYSTEM / Secreted / Virulence | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Garcia, B.L. / Geisbrecht, B.V. / Summers, B.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Diversity in the C3b Convertase Contact Residues and Tertiary Structures of the Staphylococcal Complement Inhibitor (SCIN) Protein Family. Authors: Garcia, B.L. / Summers, B.J. / Lin, Z. / Ramyar, K.X. / Ricklin, D. / Kamath, D.V. / Fu, Z.Q. / Lambris, J.D. / Geisbrecht, B.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t46.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t46.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t46.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t46_validation.pdf.gz | 419.6 KB | Display | wwPDB validaton report |
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Full document | 3t46_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | 3t46_validation.xml.gz | 6 KB | Display | |
Data in CIF | 3t46_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t46 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t46 | HTTPS FTP |
-Related structure data
Related structure data | 3t47C 3t48SC 3t49C 3t4aC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10256.391 Da / Num. of mol.: 1 / Fragment: UNP residues 29-114 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: SAV0229, SAV_0229 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99WZ4, UniProt: A0A0H3JPM4*PLUS | ||
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#2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.54 Å3/Da / Density % sol: 20.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 10mg/ml protein, 0.1M bis-Tris, 15% w/v PEG 3350, pH 4.8, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å |
Detector | Type: MARMOSAIC 330 mm CCD / Detector: CCD / Date: Aug 6, 2010 / Details: mirror |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97243 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 11553 / Num. obs: 11413 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.282 / % possible all: 95.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T48 Resolution: 1.5→24.993 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8496 / SU ML: 0.17 / σ(F): 1.53 / Phase error: 20.32 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.53 Å / VDW probe radii: 0.7 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.099 Å2 / ksol: 0.491 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.37 Å2 / Biso mean: 16.3075 Å2 / Biso min: 4.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→24.993 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: 8
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