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- PDB-1bch: MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGH) COMPLEXED WITH N-ACETYL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1bch | |||||||||
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Title | MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGH) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE | |||||||||
![]() | MANNOSE-BINDING PROTEIN-A | |||||||||
![]() | 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 | ![]() ![]() | |||||||||
![]() | Kolatkar, A.R. / Weis, W.I. | |||||||||
![]() | ![]() 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: ![]() Title: Selective Sugar Binding to the Carbohydrate Recognition Domains of the Rat Hepatic and Macrophage Asialoglycoprotein Receptors Authors: Iobst, S.T. / Drickamer, K. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.6 KB | Display | ![]() |
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PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bcjC ![]() 1afbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 3 molecules 123
#1: Protein | Mass: 17062.338 Da / Num. of mol.: 3 / Fragment: CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226 Mutation: E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: THE BACTERIALLY EXPRESSED MATERIAL WAS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS Plasmid: PINIIIOMPA2 / Production host: ![]() ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/A2G.gif)
![](data/chem/img/NGA.gif)
![](data/chem/img/NGA.gif)
#2: Sugar | ChemComp-A2G / |
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#5: Sugar |
-Non-polymers , 4 types, 339 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #4: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1996 |
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→30 Å / Num. obs: 42942 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2→2.09 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 4.8 / Rsym value: 0.272 / % possible all: 97 |
Reflection shell | *PLUS % possible obs: 97 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AFB Resolution: 2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2657.155 / 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: 37.7 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 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: 0.273 |