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Open data
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Basic information
Entry | Database: PDB / ID: 3pog | ||||||
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Title | Crystal structure of the MASP-1 CUB2 domain bound to Ca2+ | ||||||
![]() | Mannan-binding lectin serine protease 1 | ||||||
![]() | HYDROLASE / CUB domain / Ca2+ binding site / complement protein / lectin pathway of complement / MBL / MBP / ficolins / Bloodstream | ||||||
Function / homology | ![]() 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 ...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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Gingras, A.R. / Moody, P.C.E. / Wallis, R. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.1 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.4 KB | Display | ![]() |
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Full document | ![]() | 456.2 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pobC ![]() 3podC ![]() 3poeSC ![]() 3pofC ![]() 3poiC ![]() 3pojC ![]() 3ponC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13091.511 Da / Num. of mol.: 3 / Fragment: MASP-1 CUB2 domain (UNP Residues 188-301) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8CHN8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 24% PEG 8,000, 50mM Tris buffer, pH 9.0, 200mM MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 22, 2010 / Details: mirrors |
Radiation | Monochromator: optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.749→38.89 Å / Num. obs: 8258 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.26 % / Rmerge(I) obs: 0.171 / Net I/σ(I): 5.81 |
Reflection shell | Resolution: 2.749→2.91 Å / Redundancy: 2.08 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.7 / % possible all: 78.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3POE Resolution: 2.749→38.98 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.822 / SU B: 13.232 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 39.999 Å2
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Refinement step | Cycle: LAST / Resolution: 2.749→38.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.749→2.82 Å / Total num. of bins used: 20
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