+Open data
-Basic information
Entry | Database: PDB / ID: 6f1d | ||||||
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Title | CUB2 domain of C1r | ||||||
Components | Complement C1r subcomponent | ||||||
Keywords | HYDROLASE / CUB domain / EGF-like domain / complement / C1r-C1s | ||||||
Function / homology | Function and homology information complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response ...complement subcomponent C_overbar_1r_ / molecular sequestering activity / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Almitairi, J.O.M. / Venkatraman Girija, U. / Furze, C.M. / Simpson-Gray, X. / Badakshi, F. / Marshall, J.E. / Mitchell, D.A. / Moody, P.C.E. / Wallis, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structure of the C1r-C1s interaction of the C1 complex of complement activation. Authors: Almitairi, J.O.M. / Venkatraman Girija, U. / Furze, C.M. / Simpson-Gray, X. / Badakshi, F. / Marshall, J.E. / Schwaeble, W.J. / Mitchell, D.A. / Moody, P.C.E. / Wallis, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f1d.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1d.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1d ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1d | HTTPS FTP |
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-Related structure data
Related structure data | 6f1cC 6f1hC 6f39C 4lorS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13417.839 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C1R / Production host: Escherichia coli (E. coli) References: UniProt: P00736, complement subcomponent C_overbar_1r_ |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-NA / |
#4: 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: 2.91 Å3/Da / Density % sol: 57.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50 mM Tris-HCl at pH 8.5 containing 25% PEG-8K, 2 mM CaCl2 and 3% 1,6-diaminohexane |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.49 Å / Num. obs: 11599 / % possible obs: 98.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.95→2 Å / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LOR Resolution: 1.95→37.542 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.51
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.42 Å2 / Biso mean: 34.3829 Å2 / Biso min: 13.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→37.542 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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