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- PDB-1rdi: MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rdi | ||||||
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Title | MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-L-FUCOPYRANOSIDE | ||||||
![]() | MANNOSE-BINDING PROTEIN-C | ||||||
![]() | LECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN | ||||||
Function / homology | ![]() Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex / phosphatidylinositol-4-phosphate binding / D-mannose binding / antiviral innate immune response / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / calcium-dependent protein binding / : / protease binding / defense response to Gram-positive bacterium / innate immune response / signaling receptor binding / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Ng, K.K.-S. / Drickamer, K. / Weis, W.I. | ||||||
![]() | ![]() Title: Structural analysis of monosaccharide recognition by rat liver mannose-binding protein. Authors: Ng, K.K. / Drickamer, K. / Weis, W.I. #1: ![]() Title: Structure of a C-Type Mannose-Binding Protein Complexed with an Oligosaccharide Authors: Weis, W.I. / Drickamer, K. / Hendrickson, W.A. #2: ![]() Title: Structure of the Calcium-Dependent Lectin Domain from a Rat Mannose-Binding Protein Determined by MAD Phasing Authors: Weis, W.I. / Kahn, R. / Fourme, R. / Drickamer, K. / Hendrickson, W.A. #3: ![]() Title: Physical Characterization and Crystallization of the Carbohydrate-Recognition Domain of a Mannose-Binding Protein from Rat Authors: Weis, W.I. / Crichlow, G.V. / Murthy, H.M.K. / Hendrickson, W.A. / Drickamer, K. #4: ![]() Title: Differential Recognition of Core and Terminal Portions of Oligosaccharide Ligands by Carbohydrate-Recognition Domains of Two Mannose-Binding Proteins Authors: Childs, R.A. / Feizi, T. / Yuen, C.-T. / Drickamer, K. / Quesenberry, M.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.1 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.6 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rdjC ![]() 1rdkC ![]() 1rdlC ![]() 1rdmC ![]() 1rdnC ![]() 1rdoC 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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Atom site foot note | 1: CIS PROLINE - PRO 1 191 / 2: CIS PROLINE - PRO 2 191 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.999787, 0.016877, 0.011914), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 1 115 .. 1 225 2 115 .. 2 225 0.267 | |
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Components
#1: Protein | Mass: 12675.127 Da / Num. of mol.: 2 / Fragment: SUBTILISIN FRAGMENT (RESIDUES 114 - 226) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: THE BACTERIALLY EXPRESSED MATERIAL IS DIGESTED WITH SUBTILISIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS Organ: LIVER / Plasmid: PINIIIOMPA2 / Production host: ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 / Details: pH 7.4, 20% MPD USED AS A CRYOPROTECTANT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 8, 1995 |
Radiation | Monochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→10 Å / Num. obs: 24379 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.054 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
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Processing
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Refinement | Resolution: 1.8→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 20.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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