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- PDB-3t49: Crystal structure of truncated form of Staphylococcal Complement ... -
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Open data
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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 | ||||||
![]() | Fibrinogen-binding protein | ||||||
![]() | IMMUNE SYSTEM / Secreted / Virulence | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Garcia, B.L. / Geisbrecht, B.V. / Summers, B.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.4 KB | Display | ![]() |
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PDB format | ![]() | 154.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.5 KB | Display | ![]() |
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Full document | ![]() | 470 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3t46C ![]() 3t47C ![]() 3t48C ![]() 3t4aC ![]() 2qffS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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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.) ![]() ![]() Strain: Mu50 / Gene: SAV1159 / Plasmid: pT7HMT / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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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