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Yorodumi- PDB-3u4z: Crystal Structure of the Tetrahymena telomerase processivity fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u4z | ||||||
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Title | Crystal Structure of the Tetrahymena telomerase processivity factor Teb1 OB-B | ||||||
Components | Telomerase-associated protein 82 | ||||||
Keywords | DNA BINDING PROTEIN / tetrahymena / telomerase / Teb1 / processivity factor | ||||||
Function / homology | Function and homology information single-stranded telomeric DNA binding / telomerase holoenzyme complex / telomere maintenance via telomerase / chromosome, telomeric region / zinc ion binding Similarity search - Function | ||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Zeng, Z. / Huang, J. / Yang, Y. / Lei, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Structural basis for Tetrahymena telomerase processivity factor Teb1 binding to single-stranded telomeric-repeat DNA. Authors: Zeng, Z. / Min, B. / Huang, J. / Hong, K. / Yang, Y. / Collins, K. / Lei, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u4z.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u4z.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 3u4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u4z_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 3u4z_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 3u4z_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 3u4z_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/3u4z ftp://data.pdbj.org/pub/pdb/validation_reports/u4/3u4z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13018.720 Da / Num. of mol.: 2 / Fragment: unp residues 375-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Gene: TAP82 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D2CVN6 #2: 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: 2.49 Å3/Da / Density % sol: 50.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 3.6 M Na-Formate, vapor diffusion, sitting drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→100 Å / Num. obs: 10731 / % possible obs: 93.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Χ2: 1.52 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→28.592 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7632 / SU ML: 0.36 / σ(F): 1.33 / Phase error: 30.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.702 Å2 / ksol: 0.417 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.28 Å2 / Biso mean: 33.0332 Å2 / Biso min: 11.57 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→28.592 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: 8
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