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Yorodumi- PDB-2ion: Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ion | ||||||
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Title | Crystal structure of the C-terminal MA3 domain of Pdcd4 (mouse); form2 | ||||||
Components | Programmed Cell Death 4, Pdcd4 | ||||||
Keywords | ANTITUMOR PROTEIN / alpha-helical | ||||||
Function / homology | Function and homology information epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / positive regulation of endothelial cell apoptotic process / response to alkaloid / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / positive regulation of endothelial cell apoptotic process / response to alkaloid / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cytokine production involved in inflammatory response / BMP signaling pathway / response to hormone / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / apoptotic process / RNA binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||
Authors | Wlodawer, A. / LaRonde-LeBlanc, N.A. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2007 Title: Structural basis for inhibition of translation by the tumor suppressor pdcd4. Authors: Laronde-Leblanc, N. / Santhanam, A.N. / Baker, A.R. / Wlodawer, A. / Colburn, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ion.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ion.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 2ion.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ion_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 2ion_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 2ion_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2ion_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/2ion ftp://data.pdbj.org/pub/pdb/validation_reports/io/2ion | HTTPS FTP |
-Related structure data
Related structure data | 2iolSC 2iosC 2nszC 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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-Components
#1: Protein | Mass: 17563.117 Da / Num. of mol.: 1 / Fragment: C-terminal MA3 domain, residues 322-450 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd4, MA-3 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosette(DE3)pLysS / References: UniProt: Q61823 |
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#2: Chemical | ChemComp-GOL / |
#3: 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: 2.84 Å3/Da / Density % sol: 56.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.17 M ammonium sulfate, 0.085 M sodium acetate, 25.5% (w/v) PEG 2000 MME, 15% (v/v) glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→30 Å / Num. all: 24343 / Num. obs: 23715 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rsym value: 0.08 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.571→1.612 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 1605 / Rsym value: 0.501 / % possible all: 95.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IOL, Chain A Resolution: 1.57→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.251 / SU ML: 0.046 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 15.253 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.57→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.571→1.612 Å / Total num. of bins used: 20
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