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Yorodumi- PDB-2vc8: Crystal structure of the LSm domain of human EDC3 (enhancer of de... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vc8 | ||||||
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Title | Crystal structure of the LSm domain of human EDC3 (enhancer of decapping 3) | ||||||
Components | ENHANCER OF MRNA-DECAPPING PROTEIN 3 | ||||||
Keywords | PROTEIN BINDING / P-BODY COMPONENT / ENHANCER OF MRNA DECAPPING / RNA / CYTOPLASM / SM-LIKE PROTEIN / PROTEIN-BINDING | ||||||
Function / homology | Function and homology information deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / P-body assembly / P-body / cytoplasmic ribonucleoprotein granule / mRNA binding / membrane / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å | ||||||
Authors | Tritschler, F. / Hartmann, M.D. / Weichenrieder, O. | ||||||
Citation | Journal: Mol.Cell.Biol. / Year: 2007 Title: A Divergent Sm Fold in Edc3 Proteins Mediates Dcp1 Binding and P-Body Targeting. Authors: Tritschler, F. / Eulalio, A. / Truffault, V. / Hartmann, M.D. / Helms, S. / Schmidt, S. / Coles, M. / Izaurralde, E. / Weichenrieder, O. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vc8.cif.gz | 39.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vc8.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/2vc8 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/2vc8 | 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
#1: Protein | Mass: 8988.077 Da / Num. of mol.: 1 / Fragment: LSM DOMAIN, RESIDUES 1-82 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) ROSETTA II / References: UniProt: Q96F86 |
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#2: Water | ChemComp-HOH / |
Sequence details | THE CRYSTALLIZED SEQUENCE CORRESPONDS TO RESIDUES 1-82 OF HUMAN EDC3 PLUS TWO N-TERMINAL RESIDUES ...THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.6 % / Description: NONE |
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Crystal grow | pH: 4.1 Details: 40 MM NA-PROPIONATE, 20 MM NA-CACODYLATE, 40 MM BIS-TRIS-PROPANE, PH=4.1, 32% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 9, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→18.7 Å / Num. obs: 15783 / % possible obs: 98.6 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.31→1.33 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.31→18.65 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.467 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.066 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.31→18.65 Å
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Refine LS restraints |
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