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Yorodumi- PDB-1fih: N-ACETYLGALACTOSAMINE BINDING MUTANT OF MANNOSE-BINDING PROTEIN A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fih | ||||||
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Title | N-ACETYLGALACTOSAMINE BINDING MUTANT OF MANNOSE-BINDING PROTEIN A (QPDWG-HDRPY), COMPLEX WITH N-ACETYLGALACTOSAMINE | ||||||
Components | MANNOSE-BINDING PROTEIN A | ||||||
Keywords | 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 / SYNCHROTRON / Resolution: 1.95 Å | ||||||
Authors | Feinberg, H. / Torgerson, D. / Drickamer, K. / Weis, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fih.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fih.ent.gz | 85.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fih_validation.pdf.gz | 478.3 KB | Display | wwPDB validaton report |
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Full document | 1fih_full_validation.pdf.gz | 489 KB | Display | |
Data in XML | 1fih_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 1fih_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/1fih ftp://data.pdbj.org/pub/pdb/validation_reports/fi/1fih | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The bioligical assembly is a trimer. The trimer is contained in the asymmetric unit |
-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.) Rattus norvegicus (Norway rat) / Organ: LIVER / Plasmid: PINIIIOMPA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19999 #2: Sugar | ChemComp-NGA / #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: 3.17 Å3/Da / Density % sol: 61.23 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 13.5% Polyethylene glycol 8000 100 mM Tris-HCL 10 mM NaCl 20 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
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→30 Å / Num. all: 47079 / Num. obs: 43653 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.328 / Num. unique all: 4374 / % possible all: 92.7 |
Reflection | *PLUS Num. measured all: 173378 |
Reflection shell | *PLUS % possible obs: 92.7 % |
-Processing
Software |
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Refinement | Resolution: 1.95→28.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1726845.31 / 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: 44.43 Å2 / ksol: 0.357 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→28.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8.3 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 39.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.331 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.283 |