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Yorodumi- PDB-3t49: Crystal structure of truncated form of Staphylococcal Complement ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t49 | ||||||
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Title | Crystal structure of truncated form of Staphylococcal Complement Inhibitor B (SCIN-B) at 1.5 Angstrom | ||||||
Components | Fibrinogen-binding protein | ||||||
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: 1.45 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 | 3t49.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t49.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 3t49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t49 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t49 | HTTPS FTP |
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-Related structure data
Related structure data | 3t46C 3t47C 3t48C 3t4aC 2qffS 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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Unit cell |
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-Components
#1: Protein | Mass: 8214.452 Da / Num. of mol.: 4 / Fragment: SCIN-B, residues 49-116 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: SAV1159 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99UU9, UniProt: A0A0H3JZ23*PLUS #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #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: 2.74 Å3/Da / Density % sol: 55.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.5 Details: 12mg/ml protein, 0.1M sodium citrate, 1M ammonium sulfate, pH 3.5, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2010 / Details: mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7 % / Av σ(I) over netI: 30.29 / Number: 436966 / Rmerge(I) obs: 0.058 / Χ2: 1.01 / D res high: 1.45 Å / D res low: 50 Å / Num. obs: 62067 / % possible obs: 98.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.45→50 Å / Num. all: 64317 / Num. obs: 62067 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Χ2: 1.013 / Net I/σ(I): 9.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QFF Resolution: 1.45→23.927 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.9098 / SU ML: 0.13 / σ(F): 0 / Phase error: 15.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.778 Å2 / ksol: 0.437 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.27 Å2 / Biso mean: 19.5499 Å2 / Biso min: 6.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→23.927 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: 14
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