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Yorodumi- PDB-2qos: Crystal structure of complement protein C8 in complex with a pept... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qos | ||||||
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Title | Crystal structure of complement protein C8 in complex with a peptide containing the C8 binding site on C8 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Beta barrel / lipocalin / Cleavage on pair of basic residues / Complement alternate pathway / Complement pathway / Cytolysis / EGF-like domain / Glycoprotein / Immune response / Innate immunity / Membrane attack complex / Polymorphism / Secreted | ||||||
Function / homology | Function and homology information Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / complement activation / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle ...Terminal pathway of complement / membrane attack complex / complement binding / complement activation, alternative pathway / complement activation / retinol binding / complement activation, classical pathway / Regulation of Complement cascade / positive regulation of immune response / blood microparticle / killing of cells of another organism / immune response / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 Å | ||||||
Authors | Lovelace, L.L. / Chiswell, B. / Slade, D.J. / Sodetz, J.M. / Lebioda, L. | ||||||
Citation | Journal: Mol.Immunol. / Year: 2008 Title: Crystal structure of complement protein C8gamma in complex with a peptide containing the C8gamma binding site on C8alpha: Implications for C8gamma ligand binding. Authors: Lovelace, L.L. / Chiswell, B. / Slade, D.J. / Sodetz, J.M. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qos.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qos.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/2qos ftp://data.pdbj.org/pub/pdb/validation_reports/qo/2qos | HTTPS FTP |
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-Related structure data
Related structure data | 2oveS 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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Unit cell |
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-Components
#1: Protein | Mass: 19171.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C8G / Production host: Escherichia coli (E. coli) / References: UniProt: Q14CU0, UniProt: P07360*PLUS |
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#2: Protein/peptide | Mass: 1388.527 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence has been modified from the human / References: UniProt: P07357 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 26-28% PEG6K, 0.1M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97531 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97531 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. all: 20571 / Num. obs: 19234 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.051 / Χ2: 1.678 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1454 / Χ2: 1.15 / % possible all: 73.1 |
-Processing
Software |
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Refinement | Starting model: 2OVE Resolution: 1.81→37.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 64.701 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.107 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→37.6 Å
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Refine LS restraints |
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Xplor file |
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