+Open data
-Basic information
Entry | Database: PDB / ID: 1kx1 | |||||||||
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Title | Rat mannose protein A complexed with Man6-GlcNAc2-Asn | |||||||||
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: 2.8 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 | 1kx1.cif.gz | 184.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kx1.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kx1_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 1kx1_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1kx1_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 1kx1_validation.cif.gz | 52.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kx1 ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kx1 | HTTPS FTP |
-Related structure data
Related structure data | 1kwtC 1kwuC 1kwvC 1kwwC 1kwxC 1kwyC 1kwzC 1kx0C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16478.674 Da / Num. of mol.: 6 / 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: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CA / #4: Sugar | #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: 4.29 Å3/Da / Density % sol: 71.33 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 8000, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 5mg/ml in 10mM Tris-Cl pH=8.0, 10 mM NaCl, 20mM CaCl2, 1.1mM Man6GlcNAc2Asn. VAPOR DIFFUSION, HANGING DROP at 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 / Date: Dec 8, 1995 |
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: 2.8→50 Å / Num. all: 40098 / Num. obs: 37844 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Rsym value: 0.044 |
Reflection shell | Resolution: 2.8→2.93 Å / Rsym value: 0.163 / % possible all: 75.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→37.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1303812.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7975 Å2 / ksol: 0.433024 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→37.04 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.8 Å / Total num. of bins used: 6 /
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Xplor file |
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Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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