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Open data
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Basic information
Entry | Database: PDB / ID: 2j64 | ||||||
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Title | H-ficolin | ||||||
![]() | FICOLIN-3 | ||||||
![]() | LECTIN / COLLAGEN / IMMUNOLOGY / GLYCOPROTEIN / IMMUNE SYSTEM / HYDROXYLATION | ||||||
Function / homology | ![]() negative regulation of RNA biosynthetic process / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / negative regulation of viral entry into host cell / carbohydrate derivative binding / collagen trimer ...negative regulation of RNA biosynthetic process / recognition of apoptotic cell / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / negative regulation of viral entry into host cell / carbohydrate derivative binding / collagen trimer / serine-type endopeptidase complex / complement activation / Initial triggering of complement / antigen binding / carbohydrate binding / collagen-containing extracellular matrix / defense response to virus / blood microparticle / external side of plasma membrane / signaling receptor binding / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garlatti, V. / Gaboriaud, C. | ||||||
![]() | ![]() Title: Structural Insights Into the Innate Immune Recognition Specificities of L- and H-Ficolins. Authors: Garlatti, V. / Belloy, N. / Martin, L. / Lacroix, M. / Matsushita, M. / Endo, Y. / Fujita, T. / Fontecilla-Camps, J.C. / Arlaud, G.J. / Thielens, N.M. / Gaboriaud, C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143.4 KB | Display | ![]() |
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PDB format | ![]() | 112.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.9 KB | Display | ![]() |
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Full document | ![]() | 459.3 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j0gC ![]() 2j0hC ![]() 2j0yC ![]() 2j1gC ![]() 2j2pC ![]() 2j3fC ![]() 2j3gSC ![]() 2j3oC ![]() 2j3uC ![]() 2j5zC ![]() 2j60C ![]() 2j61C 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25113.809 Da / Num. of mol.: 3 / Fragment: BINDING DOMAIN, RESIDUES 89-299 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.75 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 5, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.2 Å / Num. obs: 35612 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2J3G Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.551 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.293 / ESU R Free: 0.235 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40 Å
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Refine LS restraints |
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