[English] 日本語
Yorodumi- PDB-2w95: STructure of the Discoidin I from Dictyostelium discoideum in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w95 | ||||||
---|---|---|---|---|---|---|---|
Title | STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution | ||||||
Components | DISCOIDIN-1 SUBUNIT A | ||||||
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 / asexual reproduction / N-acetylgalactosamine binding / 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 / asexual reproduction / N-acetylgalactosamine binding / 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 / cytoskeleton organization / phagocytic vesicle / extracellular matrix / response to bacterium / cell-cell adhesion / cell cortex / carbohydrate binding / regulation of gene expression / cell adhesion / cell surface / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w95.cif.gz | 186.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w95.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 2w95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w95_validation.pdf.gz | 490.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2w95_full_validation.pdf.gz | 492.1 KB | Display | |
Data in XML | 2w95_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 2w95_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w95 ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w95 | HTTPS FTP |
-Related structure data
Related structure data | 2w94SC 2wn2C 2wn3C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
-Protein / Sugars , 2 types, 6 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 #2: Sugar | |
---|
-Non-polymers , 6 types, 1071 molecules
#3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-NI / | #8: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | 2-METHYL-2,4-PENTANEDIOSequence details | THE FIRST RESIDUE IS A RESULT OF THE CLEAVAGE OF THE N- TERMINAL HISTAG | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 1.5 M LISO4, 100 MM NA HEPES PH 7.5, SUGAR SOAKED IN THE CRYSTAL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 6, 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: 1.75→47.4 Å / Num. obs: 86561 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.75→1.79 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2W94 Resolution: 1.75→47.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.008 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13.63 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→47.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|