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Yorodumi- PDB-2vm9: Native structure of the recombinant discoidin II of Dictyostelium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vm9 | ||||||
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Title | Native structure of the recombinant discoidin II of Dictyostelium discoideum at 1.75 angstrom | ||||||
Components | DISCOIDIN-2Discoidin domain | ||||||
Keywords | CELL ADHESION / DDR / LECTIN / AGGREGATION | ||||||
Function / homology | Function and homology information adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / spore wall / N-acetylgalactosamine binding / protein complex involved in cell adhesion / galactoside binding / oligosaccharide binding / polysaccharide binding / phagocytic vesicle / cytoskeleton organization / extracellular matrix ...adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / spore wall / N-acetylgalactosamine binding / protein complex involved in cell adhesion / galactoside binding / oligosaccharide binding / polysaccharide binding / phagocytic vesicle / cytoskeleton organization / extracellular matrix / response to bacterium / cell-cell adhesion / carbohydrate binding / vesicle / cell adhesion / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Aragao, K.S. / Satre, M. / Imberty, A. / Varrot, A. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Structure Determination of Discoidin II from Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain. Authors: Aragao, K.S. / Satre, M. / Imberty, A. / Varrot, A. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vm9.cif.gz | 70.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vm9.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vm9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vm9 ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vm9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28605.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2 / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P42530 |
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-Non-polymers , 5 types, 379 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 200 MM AMMONIUM PHOSPHATE MONOBASIC, 100 MM TRIS PH 8.5, 50 % MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→37 Å / Num. obs: 34043 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 11 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MERCURY STRUCTURE Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.628 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1-5 ARE DISORDERED. DISORDERED SIDE CHAIN WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.21 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→40 Å
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Refine LS restraints |
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