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- PDB-1afd: STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS -
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Open data
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Basic information
Entry | Database: PDB / ID: 1afd | ||||||
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Title | STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS | ||||||
![]() | 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: Structural basis of galactose recognition by C-type animal lectins. Authors: Kolatkar, A.R. / Weis, W.I. #1: ![]() Title: Trimeric Structure of a C-Type Mannose-Binding Protein Authors: Weis, W.I. / Drickamer, K. #2: ![]() Title: Binding of Sugar Ligands to Ca+2-Dependent Animal Lectins II. Generation of High-Affinity Galactose Binding by Site-Directed Mutagenesis Authors: Iobst, S.T. / Drickamer, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.9 KB | Display | ![]() |
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PDB format | ![]() | 86.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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Atom site foot note | 1: CIS PROLINE - PRO 1 186 / 2: CIS PROLINE - PRO 2 186 / 3: CIS PROLINE - PRO 3 186 | ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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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 2 73 .. 2 226 1 73 .. 1 226 0.630 M2 3 73 .. 3 226 1 73 .. 1 226 0.307 THE TRANSFORMATIONS WERE DERIVED BY LEAST-SQUARES SUPERPOSITION OF THE MAIN CHAIN N, CA, C, O, CB, WHERE PRESENT, OF RESIDUES 73 TO 226. |
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Components
#1: Protein | Mass: 17025.295 Da / Num. of mol.: 3 / Fragment: CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226) Mutation: E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Source method: isolated from a genetically manipulated source Details: PH 8.0, DATA COLLECTED AT 100K, 20% 2-METHYL,2-4 PENTANEDIOL (CRYOPROTECTANT) Source: (gene. exp.) ![]() ![]() Description: THE BACTERIALLY EXPRESSED MATERIAL IS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS Plasmid: PINIIIOMPA2 / Production host: ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | INSERTION INSERTED AFTER POSITION SER 191 AND RESIDUES NUMBERED CONSECUTIV | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.93 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 68 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / 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: Jul 6, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 40725 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.049 |
Reflection | *PLUS Num. obs: 41049 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 92.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.214 |
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Processing
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Refinement | Resolution: 2→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 34.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 39913 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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