+Open data
-Basic information
Entry | Database: PDB / ID: 3bla | ||||||
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Title | Synthetic Gene Encoded DcpS bound to inhibitor DG153249 | ||||||
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: 2.6 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 | 3bla.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bla.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 3bla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bla ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bla | HTTPS FTP |
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-Related structure data
Related structure data | 3bl7C 3bl9C 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 | #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: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: PEG 3350, Ammonium Formate, vapor diffusion, hanging drop, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 27, 2007 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 2 % / Av σ(I) over netI: 7.5 / Number: 31341 / Rmerge(I) obs: 0.104 / Χ2: 1.64 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 15959 / % possible obs: 96.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.6→50 Å / Num. obs: 15959 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rsym value: 0.104 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Num. unique all: 1567 / Rsym value: 0.467 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ST0 Resolution: 2.6→32.84 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.179 / SU B: 14.791 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.422 / 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: 27.094 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→32.84 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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