+Open data
-Basic information
Entry | Database: PDB / ID: 2xvs | ||||||
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Title | Crystal structure of human TTC5 (Strap) C-terminal OB domain | ||||||
Components | TETRATRICOPEPTIDE REPEAT PROTEIN 5 | ||||||
Keywords | ANTITUMOR PROTEIN / P53 COFACTOR / STRESS-RESPONSE / P300 | ||||||
Function / homology | Function and homology information positive regulation of mRNA catabolic process / cellular response to starvation / Regulation of TP53 Activity through Methylation / ribosome binding / cytoplasmic vesicle / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / positive regulation of transcription by RNA polymerase II ...positive regulation of mRNA catabolic process / cellular response to starvation / Regulation of TP53 Activity through Methylation / ribosome binding / cytoplasmic vesicle / mitochondrial matrix / DNA repair / DNA damage response / chromatin binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Adams, J. / Pike, A.C.W. / Maniam, S. / Sharpe, T.D. / Coutts, A.S. / Knapp, S. / La Thangue, B. / Bullock, A.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: The P53 Cofactor Strap Exhibits an Unexpected Tpr Motif and Oligonucleotide-Binding (Ob)-Fold Structure. Authors: Adams, C.J. / Pike, A.C. / Maniam, S. / Sharpe, T.D. / Coutts, A.S. / Knapp, S. / La Thangue, N.B. / Bullock, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xvs.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xvs.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 2xvs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/2xvs ftp://data.pdbj.org/pub/pdb/validation_reports/xv/2xvs | 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
#1: Protein | Mass: 18182.023 Da / Num. of mol.: 1 / Fragment: OLIGONUCLEOTIDE-BINDING DOMAIN, RESIDUES 262-424 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q8N0Z6 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-CL / | #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: 2.05 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.18M SODIUM IODIDE, 0.02M SODIUM ACETATE, 20% PEG3350, 10% ETHYLENE GLYCOL, 0.45% DMSO, 0.1M BIS-TRIS-PROPANE PH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 6, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.3 Å / Num. obs: 14246 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→78.77 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.919 / SU B: 5.787 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.139 / 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: 18.906 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→78.77 Å
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