+Open data
-Basic information
Entry | Database: PDB / ID: 4j7n | ||||||
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Title | Crystal structure of mouse DXO in complex with M7GPPPG cap | ||||||
Components | Protein Dom3Z | ||||||
Keywords | HYDROLASE / Decapping / 5'-3' exoribonuclease | ||||||
Function / homology | Function and homology information RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / NAD-cap decapping / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / mRNA binding / magnesium ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.5 Å | ||||||
Authors | Kilic, T. / Chang, J.H. / Tong, L. | ||||||
Citation | Journal: Mol.Cell / Year: 2013 Title: A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing. Authors: Jiao, X. / Chang, J.H. / Kilic, T. / Tong, L. / Kiledjian, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j7n.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j7n.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 4j7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j7n_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4j7n_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4j7n_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 4j7n_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/4j7n ftp://data.pdbj.org/pub/pdb/validation_reports/j7/4j7n | HTTPS FTP |
-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: 43132.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dom3z, Ng6 / Production host: Escherichia coli (E. coli) / References: UniProt: O70348 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-9MG / | #4: Chemical | #5: 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: 2.47 Å3/Da / Density % sol: 50.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 66690 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.9 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 1.5→40.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 512189.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.0016 Å2 / ksol: 0.42 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→40.51 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Xplor file |
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