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Open data
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Basic information
Entry | Database: PDB / ID: 1kmb | ||||||
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Title | SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A | ||||||
![]() | MANNOSE-BINDING PROTEIN-A | ||||||
![]() | LECTIN | ||||||
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 | ![]() ![]() | ||||||
![]() | Ng, K.K.-S. / Weis, W.I. | ||||||
![]() | ![]() Title: Structure of a selectin-like mutant of mannose-binding protein complexed with sialylated and sulfated Lewis(x) oligosaccharides. Authors: Ng, K.K. / Weis, W.I. #1: ![]() Title: Introduction of Selectin-Like Binding Specificity Into a Homologous Mannose-Binding Protein Authors: Blanck, O. / Iobst, S.T. / Gabel, C. / Drickamer, K. #2: ![]() Title: Trimeric Structure of a C-Type Mannose-Binding Protein Authors: Weis, W.I. / 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 | ![]() | 108.2 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2kmbC ![]() 3kmbC ![]() 4kmbC ![]() 1rtmS 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
#1: Protein | Mass: 16569.910 Da / Num. of mol.: 3 / Fragment: CLOSTRIPAIN FRAGMENT / Mutation: A211K, S212K, H213K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE PURIFIED PROTEIN WAS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE FRAGMENT USED IN THE CRYSTAL ...THE PURIFIED PROTEIN WAS DIGESTED WITH CLOSTRIPAI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 68 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 8-10% PEG 8000, 2% PEG 1000, 1 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTION, THE CRYSTAL WAS ADAPTED TO THE MOTHER LIQUOR PLUS 20% MPD. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 IIC / Detector: IMAGE PLATE / Date: Mar 8, 1996 / Details: COLLIMATOR |
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→40 Å / Num. obs: 36862 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.276 / % possible all: 99 |
Reflection shell | *PLUS % possible obs: 99 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RTM Resolution: 2.1→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.29 |