+Open data
-Basic information
Entry | Database: PDB / ID: 2hwx | ||||||
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Title | Structure of human SMG6 E1282C PIN domain mutant. | ||||||
Components | Telomerase-binding protein EST1A | ||||||
Keywords | RNA BINDING PROTEIN / RNA degradation / decay / NMD / EST1A / P bodies | ||||||
Function / homology | Function and homology information regulation of dephosphorylation / regulation of telomerase activity / negative regulation of telomere capping / regulation of telomere maintenance via telomerase / telomerase RNA binding / telomerase holoenzyme complex / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...regulation of dephosphorylation / regulation of telomerase activity / negative regulation of telomere capping / regulation of telomere maintenance via telomerase / telomerase RNA binding / telomerase holoenzyme complex / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / ribonucleoprotein complex binding / DNA polymerase binding / RNA endonuclease activity / chromosome, telomeric region / Hydrolases; Acting on ester bonds / nucleolus / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.9 Å | ||||||
Authors | Glavan, F. / Behm-Ansmant, I. / Izaurralde, E. / Conti, E. | ||||||
Citation | Journal: Embo J. / Year: 2006 Title: Structures of the PIN domains of SMG6 and SMG5 reveal a nuclease within the mRNA surveillance complex. Authors: Glavan, F. / Behm-Ansmant, I. / Izaurralde, E. / Conti, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hwx.cif.gz | 49.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hwx.ent.gz | 35.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/2hwx ftp://data.pdbj.org/pub/pdb/validation_reports/hw/2hwx | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20566.730 Da / Num. of mol.: 1 / Fragment: PIN domain / Mutation: E1282C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EST1A / Plasmid: pGEXcs / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL 21 / References: UniProt: Q86US8 |
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#2: 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: 2.31 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 20% Jeffamine 2000, 0.1M Hepes 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 6, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 15634 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 6.5 / Redundancy: 6.9 % / Rsym value: 0.04 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 6.9 % / Rsym value: 0.11 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 2.934 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.145 / 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: 12.924 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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