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Yorodumi- PDB-3l3o: Staphylococcal Complement Inhibitor (SCIN) in complex with Human ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l3o | ||||||
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Title | Staphylococcal Complement Inhibitor (SCIN) in complex with Human Complement Component C3c | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Complement alternate pathway / Complement pathway / Converstase / Immune response / Inflammatory response / Innate immunity / Secreted / Virulence / Immune evasion | ||||||
Function / homology | Function and homology information oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway ...oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Alternative complement activation / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / complement activation, classical pathway / Peptide ligand-binding receptors / fatty acid metabolic process / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / G alpha (i) signalling events / blood microparticle / secretory granule lumen / immune response / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.405 Å | ||||||
Authors | Geisbrecht, B.V. / Garcia, B.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Molecular Basis for Complement Recognition and Inhibition Determined by Crystallographic Studies of the Staphylococcal Complement Inhibitor (SCIN) Bound to C3c and C3b. Authors: Garcia, B.L. / Ramyar, K.X. / Tzekou, A. / Ricklin, D. / McWhorter, W.J. / 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 | 3l3o.cif.gz | 488 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l3o.ent.gz | 389.6 KB | Display | PDB format |
PDBx/mmJSON format | 3l3o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/3l3o ftp://data.pdbj.org/pub/pdb/validation_reports/l3/3l3o | HTTPS FTP |
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-Related structure data
Related structure data | 3l5nC 3nmsC 3ohxC 2a74S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 71393.320 Da / Num. of mol.: 2 / Fragment: residues 23-667 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #2: Protein | Mass: 23621.244 Da / Num. of mol.: 2 / Fragment: residues 749-954 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #3: Protein | Mass: 10064.370 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV1942, scn / Plasmid: pt7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q931M7 #4: Protein | Mass: 39537.418 Da / Num. of mol.: 2 / Fragment: residues 1321-1663 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024 #5: Sugar | |
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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: 3 Å3/Da / Density % sol: 58.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Protein solution: 5mg/ml, 0.1M HEPES, 10% PEG 6000, 5% 2-Methyl-2,4-pentanediol, pH 7.5, 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: Jun 12, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.4 % / Av σ(I) over netI: 6.5 / Number: 152670 / Rmerge(I) obs: 0.161 / Χ2: 1.11 / D res high: 3.4 Å / D res low: 50 Å / Num. obs: 45397 / % possible obs: 97.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 3.4→50 Å / Num. all: 48213 / Num. obs: 45397 / % possible obs: 97.5 % / Observed criterion σ(F): 2.38 / Observed criterion σ(I): 2.38 / Redundancy: 3.4 % / Biso Wilson estimate: 49.8 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.38 / % possible all: 93.1 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 41.99 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2A74,2QFF Resolution: 3.405→34.522 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 2.38 / σ(F): 0.21 / Phase error: 27.44 / 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 / Bsol: 40.458 Å2 / ksol: 0.256 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.06 Å2
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Refinement step | Cycle: LAST / Resolution: 3.405→34.522 Å
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Refine LS restraints |
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LS refinement shell |
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