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Yorodumi- PDB-1ph1: CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ph1 | ||||||
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Title | CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTGGGGT | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / SINGLE STRAND DNA BINDING PROTEIN / PROTEIN DNA INTERACTIONS / SEQUENCE SPECIFICITY / NONCOGNATE / OLIGONUCLEOTIDE AND OLIGOSACCHARIDE BINDING FOLD / OB FOLD / TELOMERES / PROTEIN/DNA / 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 / nucleus Similarity search - Function | ||||||
Biological species | Sterkiella nova (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å | ||||||
Authors | Theobald, D.L. / Schultz, S.C. | ||||||
Citation | Journal: Embo J. / Year: 2003 Title: Nucleotide Shuffling and Ssdna Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes Authors: Theobald, D.L. / 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 | 1ph1.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ph1.ent.gz | 134.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ph1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ph1_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 1ph1_full_validation.pdf.gz | 465.6 KB | Display | |
Data in XML | 1ph1_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 1ph1_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/1ph1 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/1ph1 | HTTPS FTP |
-Related structure data
Related structure data | 1pa6C 1ph2C 1ph3C 1ph4C 1ph5C 1ph6C 1ph7C 1ph8C 1ph9C 1phjC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4109.652 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: CHAIN D IS SINGLE STRAND DNA. CHAINS G AND H ARE A G-QUARTET LINKED DNA DIMER. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, extra thymidine at 3'-end #2: Protein | | Mass: 52589.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: ALANINE VERSION / Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-56A AND MAC-56K AND MAC-56S / Plasmid: PKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P29549 #3: Protein | | Mass: 24584.795 Da / Num. of mol.: 1 / Fragment: residues 8-224 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-41A AND MAC-41S / Plasmid: PKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P16458 #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: 2.98 Å3/Da / Density % sol: 58.66 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging dropDetails: drop contains the same amount of reservoir solution except 50mM NaCl | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 37742 / Biso Wilson estimate: 21.6 Å2 |
Reflection | *PLUS Highest resolution: 2.5 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.106 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1090878.26 / 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: 18.7292 Å2 / ksol: 0.2985 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.51→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.51→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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