+Open data
-Basic information
Entry | Database: PDB / ID: 4h6i | ||||||
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Title | Crystal Structure of Staphylococcal Complement Inhibitor SCIN-B | ||||||
Components | Fibrinogen-binding protein | ||||||
Keywords | IMMUNE SYSTEM / Complement System / Innate Immunity / Staphylococcus aureus Structural Biology | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.091 Å | ||||||
Authors | Garcia, B.L. / Geisbrecht, B.V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: A Structurally Dynamic N-terminal Helix Is a Key Functional Determinant in Staphylococcal Complement Inhibitor (SCIN) Proteins. Authors: Garcia, B.L. / Summers, B.J. / Ramyar, K.X. / Tzekou, A. / Lin, Z. / Ricklin, D. / Lambris, J.D. / Laity, J.H. / 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 | 4h6i.cif.gz | 57.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h6i.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 4h6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h6i_validation.pdf.gz | 444.9 KB | Display | wwPDB validaton report |
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Full document | 4h6i_full_validation.pdf.gz | 449.4 KB | Display | |
Data in XML | 4h6i_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 4h6i_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/4h6i ftp://data.pdbj.org/pub/pdb/validation_reports/h6/4h6i | HTTPS FTP |
-Related structure data
Related structure data | 4h6hC 3t49S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 10123.601 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Mu50 / ATCC 700699 / Gene: SAV1159, SAV_1159 / Plasmid: pt7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99UU9, UniProt: A0A0H3JZ23*PLUS |
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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: 2.51 Å3/Da / Density % sol: 51.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 16mg/ml protein sample stored in 10mM Tris (pH 7.4), 50mM NaCl; Crystallization conditions: 0.2M AmSO4, 30% PEG 8k. Crystals appear in 5-7d, 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: Feb 1, 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: 4.6 % / Av σ(I) over netI: 18.57 / Number: 25131 / Rmerge(I) obs: 0.071 / Χ2: 1.02 / D res high: 3.1 Å / D res low: 50 Å / Num. obs: 5479 / % possible obs: 93.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 3.093→50 Å / Num. all: 5479 / Num. obs: 5479 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: STARTING MODEL 3T49 Resolution: 3.091→32.741 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 31.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 109.7075 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.091→32.741 Å
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Refine LS restraints |
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LS refinement shell |
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