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Yorodumi- PDB-1k8g: Crystal Structure of the N-terminal domain of Oxytricha nova telo... -
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-Basic information
Entry | Database: PDB / ID: 1k8g | ||||||
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Title | Crystal Structure of the N-terminal domain of Oxytricha nova telomere end binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Protein-DNA Complex / telomeres / sequence specific ssDNA binding protein / OB folds / protein single strand DNA interactions / 3'-DNA end binding protein / telomere end binding protein / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information telomere cap complex / telomerase inhibitor activity / regulation of telomere maintenance via telomerase / nuclear telomere cap complex / single-stranded telomeric DNA binding / G-rich strand telomeric DNA binding / telomere capping / protein-containing complex Similarity search - Function | ||||||
Biological species | Sterkiella nova (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Classen, S. / Ruggles, J.A. / Schultz, S.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of the N-terminal domain of Oxytricha nova telomere end-binding protein alpha subunit both uncomplexed and complexed with telomeric ssDNA. Authors: Classen, S. / Ruggles, J.A. / Schultz, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8g.cif.gz | 185.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8g.ent.gz | 146.8 KB | Display | PDB format |
PDBx/mmJSON format | 1k8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k8g_validation.pdf.gz | 479.9 KB | Display | wwPDB validaton report |
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Full document | 1k8g_full_validation.pdf.gz | 519.2 KB | Display | |
Data in XML | 1k8g_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 1k8g_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8g ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8g | HTTPS FTP |
-Related structure data
Related structure data | 1otcS S: Starting model for refinement |
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Similar 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: DNA chain | Mass: 1880.251 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 36360.074 Da / Num. of mol.: 3 / Fragment: N-terminal 35kDa ssDNA binding domain Source method: isolated from a genetically manipulated source Details: alanine version / Source: (gene. exp.) Sterkiella nova (eukaryote) / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29549 #3: Chemical | ChemComp-SO4 / #4: 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: 2.5 Å3/Da / Density % sol: 52.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000, MES, Ammonium sulfate, DTT, Sodium Azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 1999 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. all: 35994 / Num. obs: 35994 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.8 Å2 / Rsym value: 0.103 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.6→30 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.71 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 574134 / Rmerge(I) obs: 0.103 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: residues 37-320 of Oxytricha nova telomere end binding protein alpha subunit PDB accession 1OTC Resolution: 2.6→30 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 213150.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS automatically determined
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.7033 Å2 / ksol: 0.336706 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 30 Å / Num. reflection obs: 35965 / σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 46.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.6 Å / Rfactor Rfree: 0.393 / % reflection Rfree: 10 % / Rfactor Rwork: 0.328 / Rfactor obs: 0.339 |