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Open data
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Basic information
Entry | Database: PDB / ID: 2j3o | ||||||
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Title | L-ficolin complexed to N-acetyl-D-glucosamine | ||||||
![]() | FICOLIN-2 | ||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / COLLAGEN / IMMUNOLOGY / GLYCOPROTEIN | ||||||
Function / homology | ![]() mannan binding / 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 / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer ...mannan binding / 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 / opsonization / complement activation, lectin pathway / carbohydrate derivative binding / collagen trimer / serine-type endopeptidase complex / proteoglycan binding / Initial triggering of complement / antigen binding / calcium-dependent protein binding / collagen-containing extracellular matrix / defense response to Gram-negative bacterium / blood microparticle / defense response to Gram-positive bacterium / external side of plasma membrane / signaling receptor binding / proteolysis / extracellular space / extracellular exosome / 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 | ![]() | 268.5 KB | Display | ![]() |
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PDB format | ![]() | 217.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 516.6 KB | Display | ![]() |
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Full document | ![]() | 567 KB | Display | |
Data in XML | ![]() | 54.3 KB | Display | |
Data in CIF | ![]() | 73 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j0gC ![]() 2j0hC ![]() 2j0yC ![]() 2j1gC ![]() 2j2pC ![]() 2j3fC ![]() 2j3gC ![]() 2j3uC ![]() 2j5zC ![]() 2j60C ![]() 2j61C ![]() 2j64C ![]() 1jc9S 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24840.459 Da / Num. of mol.: 6 / Fragment: BINDING DOMAIN, RESIDUES 95-313 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Sequence details | C-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATES: THERE IS A DIFFERENCE BECAUSE IT ...C-TERMINAL DOMAIN CONFLICTS BETWEEN UNP SEQUENCE AND COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.29 % |
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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: Nov 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9757 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→19.76 Å / Num. obs: 57851 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1JC9 Resolution: 2.65→19 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.889 / SU B: 14.302 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.688 / ESU R Free: 0.353 / 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: 55.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→19 Å
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Refine LS restraints |
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