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- PDB-1fif: N-ACETYLGALACTOSAMINE-SELECTIVE MUTANT OF MANNOSE-BINDING PROTEIN... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1fif | ||||||
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Title | N-ACETYLGALACTOSAMINE-SELECTIVE MUTANT OF MANNOSE-BINDING PROTEIN-A (QPDWG-HDRPY) | ||||||
![]() | MANNOSE-BINDING PROTEIN-A | ||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Feinberg, H. / Torgersen, D. / Drickamer, K. / Weis, W.I. | ||||||
![]() | ![]() Title: Mechanism of pH-dependent N-acetylgalactosamine binding by a functional mimic of the hepatocyte asialoglycoprotein receptor. Authors: Feinberg, H. / Torgersen, D. / Drickamer, K. / Weis, W.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 89.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
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Full document | ![]() | 447.8 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a trimer. The complete trimer is contained in the asymmetric unit |
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Components
#1: Protein | Mass: 17185.447 Da / Num. of mol.: 3 / Fragment: RESIDUES 73-226 Mutation: E185Q, N187D, H189W, INS(Y190, G191, H192, G193, L194), S196G, T202H, I212D, A216R, S217P, H218Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.73 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 13.5% golyethylene glycol 8,000, 100 mM Tris-HCl, 10 mM NaCl, 20 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→100 Å / Num. all: 120159 / Num. obs: 42884 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.95→2.12 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.157 / Num. unique all: 4207 / % possible all: 93 |
Reflection | *PLUS Num. measured all: 120159 |
Reflection shell | *PLUS % possible obs: 93 % |
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Processing
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Refinement | Resolution: 1.95→28.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1848493.64 / 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: 45.46 Å2 / ksol: 0.333 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→28.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8.2 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.3 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 / % reflection Rfree: 8 % / Rfactor Rwork: 0.221 |