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Yorodumi- PDB-2kmb: COMPLEX OF 3'-NEUAC-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kmb | |||||||||
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Title | COMPLEX OF 3'-NEUAC-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A | |||||||||
Components | MANNOSE-BINDING PROTEIN-A | |||||||||
Keywords | LECTIN | |||||||||
Function / homology | Function and homology information 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 | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Ng, K.K.-S. / Weis, W.I. | |||||||||
Citation | Journal: Biochemistry / Year: 1997 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: Journal: J.Biol.Chem. / Year: 1996 Title: Introduction of Selectin-Like Binding Specificity Into a Homologous Mannose-Binding Protein Authors: Blanck, O. / Iobst, S.T. / Gabel, C. / Drickamer, K. #2: Journal: Structure / Year: 1994 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kmb.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kmb.ent.gz | 90.4 KB | Display | PDB format |
PDBx/mmJSON format | 2kmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/2kmb ftp://data.pdbj.org/pub/pdb/validation_reports/km/2kmb | HTTPS FTP |
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-Related structure data
Related structure data | 1kmbC 3kmbC 4kmbC 1rtmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Rattus norvegicus (Norway rat) / Plasmid: PINIIIOMPA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19999 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose / Sialyl-Lewis X antigen / beta anomer | |
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-Non-polymers , 3 types, 471 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | #6: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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 PLUS 80 MM 3'-NEUAC-LEWIS-X. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 5, 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→40 Å / Num. obs: 41761 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.264 / % possible all: 93.2 |
Reflection shell | *PLUS % possible obs: 93.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTM Resolution: 2→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: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.54 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.19 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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