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Yorodumi- PDB-1md8: Monomeric structure of the active catalytic domain of complement ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1md8 | ||||||
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Title | Monomeric structure of the active catalytic domain of complement protease C1r | ||||||
Components | C1R COMPLEMENT SERINE PROTEASE | ||||||
Keywords | HYDROLASE / complement / innate immunity / serine protease / activation / substrate specificity | ||||||
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 / serine-type peptidase activity / complement activation, classical pathway / 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 / serine-type peptidase activity / complement activation, classical pathway / 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 / Resolution: 2.8 Å | ||||||
Authors | Budayova-Spano, M. / Grabarse, W. / Thielens, N.M. / Hillen, H. / Lacroix, M. / Schmidt, M. / Fontecilla-Camps, J. / Arlaud, G.J. / Gaboriaud, C. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Monomeric structures of the zymogen and active catalytic domain of complement protease c1r: further insights into the c1 activation mechanism Authors: Budayova-Spano, M. / Grabarse, W. / Thielens, N.M. / Hillen, H. / Lacroix, M. / Schmidt, M. / Fontecilla-Camps, J. / Arlaud, G.J. / Gaboriaud, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1md8.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1md8.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 1md8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1md8_validation.pdf.gz | 430.2 KB | Display | wwPDB validaton report |
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Full document | 1md8_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 1md8_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 1md8_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1md8 ftp://data.pdbj.org/pub/pdb/validation_reports/md/1md8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 37199.027 Da / Num. of mol.: 1 / Fragment: C-terminal CCP-SP domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High FiveTM / Production host: Trichoplusia ni (cabbage looper) References: UniProt: P00736, complement subcomponent C_overbar_1r_ |
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#2: 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: 2.78 Å3/Da / Density % sol: 55.8 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: ammonium sulfate, TAPS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979549 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 9, 2001 / Details: mirrors |
Radiation | Monochromator: Monochromator can use either 111 or 311 Silicon single cristals. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979549 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→99 Å / Num. obs: 10075 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 92.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.8→2.87 Å / Rsym value: 0.189 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 25998 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.189 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→12 Å / Rfactor Rfree error: 0.012 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.0057 Å2 / ksol: 0.339214 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. reflection obs: 10191 / Rfactor Rfree: 0.2545 / Rfactor Rwork: 0.2097 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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