+Open data
-Basic information
Entry | Database: PDB / ID: 1kwx | ||||||
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Title | Rat mannose protein A complexed with b-Me-Fuc. | ||||||
Components | MANNOSE-BINDING PROTEIN A | ||||||
Keywords | IMMUNE SYSTEM / SUGAR BINDING PROTEIN / LECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN | ||||||
Function / homology | Function and homology information calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / polysaccharide binding / protein homotrimerization / D-mannose binding ...calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / polysaccharide binding / protein homotrimerization / D-mannose binding / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / calcium ion binding / protein homodimerization activity / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Orientation of bound ligands in mannose-binding proteins. Implications for multivalent ligand recognition. Authors: Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kwx.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kwx.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 1kwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kwx ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kwx | HTTPS FTP |
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-Related structure data
Related structure data | 1kwtC 1kwuC 1kwvC 1kwwC 1kwyC 1kwzC 1kx0C 1kx1C 1kzaC 1kzbC 1kzcC 1kzdC 1kzeC 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: 16478.674 Da / Num. of mol.: 3 / Fragment: residues 90-238 of P19999 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MBL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19999 #2: Sugar | #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2, 200mM b-Me-Fuc. VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-22 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 40916 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Rsym value: 0.044 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.218 / % possible all: 94.5 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / Redundancy: 3 % / Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 94.5 % / Redundancy: 2.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rwork: 0.2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d |