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Yorodumi- PDB-3pob: Crystal structure of MASP-1 CUB2 domain in complex with the colla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pob | ||||||
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Title | Crystal structure of MASP-1 CUB2 domain in complex with the collagen-like domain of MBL | ||||||
Components |
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Keywords | HYDROLASE / collagen complex / MASP / CUB domain / MBL / MBP / Collagen peptide / Calcium binding site / Complement proteins / lectin pathway of complement / MASP-1 / Bloodstream | ||||||
Function / homology | Function and homology information Scavenging by Class A Receptors / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity ...Scavenging by Class A Receptors / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / protein homodimerization activity / extracellular space Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Gingras, A.R. / Moody, P.C.E. / Wallis, R. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structural Basis of Mannan-Binding Lectin Recognition by Its Associated Serine Protease MASP-1: Implications for Complement Activation. Authors: Gingras, A.R. / Girija, U.V. / Keeble, A.H. / Panchal, R. / Mitchell, D.A. / Moody, P.C. / Wallis, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pob.cif.gz | 55.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pob.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/3pob ftp://data.pdbj.org/pub/pdb/validation_reports/po/3pob | HTTPS FTP |
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-Related structure data
Related structure data | 3podC 3poeC 3pofC 3pogC 3poiC 3pojC 3ponC 3demS 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: 13091.511 Da / Num. of mol.: 1 / Fragment: MASP-1 CUB2 domain (UNP Residues 188-301) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Crarf, MASP-1/-3, Masp1, Masp3 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8CHN8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases | ||||
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#2: Protein/peptide | Mass: 2479.700 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide #3: Chemical | ChemComp-CA / | #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: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 28% PEG 8000, 50mM Tris, pH 8.0, 4mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9184 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2010 |
Radiation | Monochromator: multi-layer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 17822 / Num. obs: 17755 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.76 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 5.38 / Num. unique all: 2795 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DEM Resolution: 1.801→26.44 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.029 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.129 Å2
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Refinement step | Cycle: LAST / Resolution: 1.801→26.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.848 Å / Total num. of bins used: 20
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