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Yorodumi- PDB-3t47: Crystal Structure of truncated form of Staphylococcal Complement ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t47 | ||||||
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Title | Crystal Structure of truncated form of Staphylococcal Complement Inhibitor D (SCIN-D) at 1.3 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: 1.301 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 | 3t47.cif.gz | 98.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t47.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 3t47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t47_validation.pdf.gz | 428.9 KB | Display | wwPDB validaton report |
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Full document | 3t47_full_validation.pdf.gz | 430.4 KB | Display | |
Data in XML | 3t47_validation.xml.gz | 9 KB | Display | |
Data in CIF | 3t47_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t4/3t47 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/3t47 | HTTPS FTP |
-Related structure data
Related structure data | 3t46C 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
#1: Protein | Mass: 9178.323 Da / Num. of mol.: 2 / Fragment: SCIN-D, residues 37-111 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / Gene: SAV0229 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99WZ4, UniProt: A0A0H3JPM4*PLUS #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: 1.95 Å3/Da / Density % sol: 36.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 10mg/ml protein, 0.1M bis-Tris, 30% PEG 8000, 20 mM sodium thiocyanate, pH 5.0, 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 300 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 | Redundancy: 18.7 % / Av σ(I) over netI: 35.61 / Number: 593190 / Rmerge(I) obs: 0.078 / Χ2: 1.05 / D res high: 1.3 Å / D res low: 50 Å / Num. obs: 31662 / % possible obs: 92.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.3→50 Å / Num. all: 32500 / Num. obs: 31662 / % possible obs: 92.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 18.7 % / Rmerge(I) obs: 0.078 / Χ2: 1.053 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Rfactor: 28.59 / Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T48 Resolution: 1.301→28.967 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.9059 / SU ML: 0.12 / σ(F): 1.38 / Phase error: 16.49 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.162 Å2 / ksol: 0.433 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.76 Å2 / Biso mean: 19.6224 Å2 / Biso min: 4.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.301→28.967 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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