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- PDB-3kmb: COMPLEX OF 3'-SULFO-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kmb | |||||||||
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Title | COMPLEX OF 3'-SULFO-LEWIS-X WITH A 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 | ![]() | 113 KB | Display | ![]() |
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PDB format | ![]() | 88.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 35.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kmbC ![]() 2kmbC ![]() 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
-Protein , 1 types, 3 molecules 123
#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.) ![]() ![]() ![]() ![]() |
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-Sugars , 3 types, 3 molecules ![](data/chem/img/FUC.gif)
#2: Polysaccharide | alpha-L-fucopyranose-(1-3)-[3-O-sulfo-beta-D-galactopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[3-O-sulfo-beta-D-galactopyranose-(1-4)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | alpha-L-fucopyranose-(1-3)-[3-O-sulfo-beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-FUC / |
-Non-polymers , 3 types, 471 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
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: PROTEIN WAS CRYSTALLIZED FROM 8-10% PEG 8000, 2% PEG 1000, 100 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTED, THE CRYSTAL WAS SOAKED IN THE MOTHER LIQUOR ...Details: PROTEIN WAS CRYSTALLIZED FROM 8-10% PEG 8000, 2% PEG 1000, 100 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTED, THE CRYSTAL WAS SOAKED IN THE MOTHER LIQUOR MINUS PEG 8000, PLUS 35% PEG 400, PLUS 80 MM 3'-SULFO- LEWIS-X. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 1996 / Details: COLLIMATOR, MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 44240 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.25 / % possible all: 95.6 |
Reflection shell | *PLUS % possible obs: 95.6 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1RTM Resolution: 1.95→10 Å / Rfactor Rfree error: 0.004 / 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: 23.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 40985 / Rfactor obs: 0.205 / Rfactor Rfree: 0.255 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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