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Yorodumi- PDB-2vme: Structure of the wild-type discoidin II from Dictyostelium discoideum -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vme | ||||||
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Title | Structure of the wild-type discoidin II from Dictyostelium discoideum | ||||||
Components | DISCOIDIN-2 | ||||||
Keywords | CELL ADHESION / LECTIN / AGGREGATION / DDR | ||||||
Function / homology | Function and homology information adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / spore wall / N-acetylgalactosamine binding / oligosaccharide binding / galactoside binding / polysaccharide binding / phagocytic vesicle / cytoskeleton organization / extracellular matrix / cell-cell adhesion ...adenylate cyclase-activating G protein-coupled cAMP receptor signaling pathway / spore wall / N-acetylgalactosamine binding / oligosaccharide binding / galactoside binding / polysaccharide binding / phagocytic vesicle / cytoskeleton organization / extracellular matrix / cell-cell adhesion / response to bacterium / carbohydrate binding / vesicle / cell adhesion / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | DICTYOSTELIUM DISCOIDEUM (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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 | 2vme.cif.gz | 315.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vme.ent.gz | 258.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vme_validation.pdf.gz | 497.1 KB | Display | wwPDB validaton report |
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Full document | 2vme_full_validation.pdf.gz | 512.7 KB | Display | |
Data in XML | 2vme_validation.xml.gz | 61.7 KB | Display | |
Data in CIF | 2vme_validation.cif.gz | 83.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vm/2vme ftp://data.pdbj.org/pub/pdb/validation_reports/vm/2vme | HTTPS FTP |
-Related structure data
Related structure data | 2vm9SC 2vmcC 2vmdC 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 28685.703 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: HIS84 IS PHOSPHORYLATED. / Source: (natural) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2 / References: UniProt: P42530 |
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-Non-polymers , 6 types, 569 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | GLYCEROL (GOL): FROM CRYOPROTEC |
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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: 2.73 Å3/Da / Density % sol: 54.95 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 20% PEG 4K, 10 MM CDCL2, 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→26.82 Å / Num. obs: 66709 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VM9 Resolution: 2.45→26.8 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.226 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.467 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.78 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→26.8 Å
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