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Yorodumi- PDB-1bcj: MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGHV) COMPLEXED WITH N-ACETY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bcj | ||||||
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Title | MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGHV) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE | ||||||
Components | MANNOSE-BINDING PROTEIN-A | ||||||
Keywords | LECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN | ||||||
Function / homology | Function and homology information calcium-dependent carbohydrate binding / oligosaccharide binding / complement activation, lectin pathway / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / polysaccharide binding / protein homotrimerization / mannose binding ...calcium-dependent carbohydrate binding / oligosaccharide binding / complement activation, lectin pathway / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / polysaccharide binding / protein homotrimerization / mannose binding / positive regulation of phagocytosis / complement activation, classical pathway / multivesicular body / 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: 2.1 Å | ||||||
Authors | Kolatkar, A.R. / Weis, W.I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Mechanism of N-acetylgalactosamine binding to a C-type animal lectin carbohydrate-recognition domain. Authors: Kolatkar, A.R. / Leung, A.K. / Isecke, R. / Brossmer, R. / Drickamer, K. / Weis, W.I. #1: Journal: J.Biol.Chem. / Year: 1996 Title: Selective Sugar Binding to the Carbohydrate Recognition Domains of the Rat Hepatic and Macrophage Asialoglycoprotein Receptors Authors: Iobst, S.T. / Drickamer, K. #2: Journal: J.Biol.Chem. / Year: 1996 Title: Structural Basis of Galactose Recognition by C-Type Animal Lectins Authors: Kolatkar, A.R. / 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 | 1bcj.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bcj.ent.gz | 86.6 KB | Display | PDB format |
PDBx/mmJSON format | 1bcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/1bcj ftp://data.pdbj.org/pub/pdb/validation_reports/bc/1bcj | HTTPS FTP |
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-Related structure data
Related structure data | 1bchC 1afbS S: Starting model for refinement 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 17074.391 Da / Num. of mol.: 3 / Fragment: CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226 Mutation: S154V, E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Description: THE BACTERIALLY EXPRESSED MATERIAL WAS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS Plasmid: PINIIIOMPA2 / 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: 3.2 Å3/Da / Density % sol: 60.9 % Description: 20% 2-METHYL,2-4 PENTANEDIOL (CRYOPROTECTANT), 200MM N-ACETYL-D-GALACTOSAMINE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 12% PEG8000, 100MM TRIS/PH8.0, 20MM CALCIUM CHLORIDE, 10MM SODIUM CHLORIDE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 35683 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.283 / % possible all: 96.9 |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AFB Resolution: 2.1→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2643.491 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3C / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.258 |