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Yorodumi- PDB-1vlr: Crystal structure of mRNA decapping enzyme (DcpS) from Mus muscul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vlr | ||||||
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Title | Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution | ||||||
Components | mRNA decapping enzyme | ||||||
Keywords | RNA BINDING PROTEIN / 16740816 / mRNA decapping enzyme (DcpS) / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information cellular response to menadione / : / mRNA decay by 3' to 5' exoribonuclease / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / negative regulation of programmed cell death / P-body / mitochondrion ...cellular response to menadione / : / mRNA decay by 3' to 5' exoribonuclease / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / negative regulation of programmed cell death / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Crystal structure of an Apo mRNA decapping enzyme (DcpS) from Mouse at 1.83 A resolution. Authors: Han, G.W. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / ...Authors: Han, G.W. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Hornsby, M. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McPhillips, T.M. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Paulsen, J. / Quijano, K. / Reyes, R. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vlr.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vlr.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vlr_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 1vlr_full_validation.pdf.gz | 445.8 KB | Display | |
Data in XML | 1vlr_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 1vlr_validation.cif.gz | 49.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/1vlr ftp://data.pdbj.org/pub/pdb/validation_reports/vl/1vlr | HTTPS FTP |
-Related structure data
Related structure data | 1st0S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40504.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: DcpS / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DAR7 #2: Chemical | ChemComp-EDO / #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: 2.35 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.2 Details: 0.2M KF, 20.0% PEG-3350, No Buffer pH 7.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 |
Detector | Type: ADSC / Detector: CCD / Date: Oct 8, 2003 |
Radiation | Monochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→37.58 Å / Num. obs: 64852 / % possible obs: 97.9 % / Redundancy: 3.69 % / Biso Wilson estimate: 24.23 Å2 / Rsym value: 0.063 / Net I/σ(I): 18.07 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 3.07 % / Mean I/σ(I) obs: 3.04 / Num. unique all: 5575 / Rsym value: 0.389 / % possible all: 84.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1st0 Resolution: 1.83→37.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.301 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS A LARGE UNMODELED PEAK IN THE DIFFERENCE MAP NEAR THE CARBONYL OXYGEN OF PRO-287 IN BOTH CHAINS.
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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: 15.046 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→37.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.825→1.873 Å / Total num. of bins used: 20
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