+Open data
-Basic information
Entry | Database: PDB / ID: 3bl7 | ||||||
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Title | Synthetic Gene Encoded DcpS bound to inhibitor DG156844 | ||||||
Components | Scavenger mRNA-decapping enzyme DcpS | ||||||
Keywords | HYDROLASE / MRNA DECAPPING ENZYME / DCPS / LIGAND COMPLEX / Cytoplasm / Nonsense-mediated mRNA decay / Nucleus / Polymorphism / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D | ||||||
Function / homology | Function and homology information mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Staker, B.L. / Christensen, J. / Stewart, L. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D) | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2008 Title: DcpS as a therapeutic target for spinal muscular atrophy. Authors: Singh, J. / Salcius, M. / Liu, S.W. / Staker, B.L. / Mishra, R. / Thurmond, J. / Michaud, G. / Mattoon, D.R. / Printen, J. / Christensen, J. / Bjornsson, J.M. / Pollok, B.A. / Kiledjian, M. ...Authors: Singh, J. / Salcius, M. / Liu, S.W. / Staker, B.L. / Mishra, R. / Thurmond, J. / Michaud, G. / Mattoon, D.R. / Printen, J. / Christensen, J. / Bjornsson, J.M. / Pollok, B.A. / Kiledjian, M. / Stewart, L. / Jarecki, J. / Gurney, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bl7.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bl7.ent.gz | 102.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bl7 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bl7 | HTTPS FTP |
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-Related structure data
Related structure data | 3bl9C 3blaC 1st0S 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: 34891.613 Da / Num. of mol.: 2 / Fragment: UNP residues 38-337 Source method: isolated from a genetically manipulated source Details: SMT3 FUSION PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Gene: DCPS, DCS1, HINT5 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96C86, Hydrolases #2: Chemical | ChemComp-DD1 / | #3: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 39.88 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: PEG 3350, Ammonium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 23, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. obs: 23402 / % possible obs: 96.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.31→2.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.43 / Num. unique all: 2293 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ST0 Resolution: 2.31→28.95 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.86 / SU B: 9.457 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.752 / ESU R Free: 0.312 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.827 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→28.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.367 Å / Total num. of bins used: 20
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