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Yorodumi- PDB-2w94: Native structure of the Discoidin I from Dictyostelium discoideum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w94 | ||||||
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Title | Native structure of the Discoidin I from Dictyostelium discoideum at 1.8 angstrom resolution | ||||||
Components | DISCOIDIN-1 SUBUNIT ADiscoidin domain | ||||||
Keywords | CELL ADHESION / H TYPE LECTIN | ||||||
Function / homology | Function and homology information lectin-induced modified bacterial internalization / lipooligosaccharide binding / response to catechin / protein localization to cell cortex / N-acetylgalactosamine binding / asexual reproduction / response to curcumin / protein complex involved in cell adhesion / symbiont cell surface / oligosaccharide binding ...lectin-induced modified bacterial internalization / lipooligosaccharide binding / response to catechin / protein localization to cell cortex / N-acetylgalactosamine binding / asexual reproduction / response to curcumin / protein complex involved in cell adhesion / symbiont cell surface / oligosaccharide binding / regulation of protein complex stability / cortical cytoskeleton organization / polysaccharide binding / intracellular vesicle / cell-substrate adhesion / mitotic cytokinesis / phagocytic vesicle / cytoskeleton organization / extracellular matrix / response to bacterium / cell-cell adhesion / cell cortex / carbohydrate binding / regulation of gene expression / cell adhesion / cell surface / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Saboia Aragao, K. / Imberty, A. / Varrot, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Discoidin I from Dictyostelium Discoideum and Interactions with Oligosaccharides: Specificity, Affinity, Crystal Structures and Comparison with Discoidin II. Authors: Mathieu, S. / Saboia Aragao, K. / 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 | 2w94.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w94.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 2w94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w94 ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w94 | HTTPS FTP |
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-Related structure data
Related structure data | 2w95C 2wn2C 2wn3C 2vm9S C: citing same article (ref.) S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 28354.576 Da / Num. of mol.: 3 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): ROSETTA2(DE3)PLYSS / References: UniProt: P02886 |
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-Non-polymers , 6 types, 994 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-NI / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 2-METHYL-2,4-PENTANEDIOSequence details | FIRST RESIDUE IS ADDED FOLLOWING THE CLEAVAGE OF THE N TERMINAL HIS TAG | |
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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: 2.46 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 1.5 M LISO4 100 MM HEPES 7.5 |
-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: Jun 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→28.6 Å / Num. obs: 29532 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VM9 Resolution: 1.8→28.6 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.447 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS 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: 15.809 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→28.6 Å
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