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Yorodumi- PDB-1ph2: CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ph2 | ||||||
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Title | CRYSTAL STRUCTURE OF THE OXYTRICHA NOVA TELOMERE END-BINDING PROTEIN COMPLEXED WITH NONCOGNATE SSDNA GGGGTTTTG | ||||||
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 / single-stranded telomeric DNA binding / nuclear telomere cap complex / 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: 3.1 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 | 1ph2.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ph2.ent.gz | 137.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ph2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ph/1ph2 ftp://data.pdbj.org/pub/pdb/validation_reports/ph/1ph2 | HTTPS FTP |
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-Related structure data
Related structure data | 1pa6C 1ph1C 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
-DNA chain , 2 types, 3 molecules GHD
#1: DNA chain | Mass: 4109.652 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: CHAINS G AND H ARE A G-QUARTET LINKED DNA DIMER. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES. #2: DNA chain | | Mass: 2817.843 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: CHAIN D IS SINGLE STRAND DNA. 3' TERMINAL SINGLE STRAND DNA SEQUENCE OF MACRONUCLEAR TELOMERES, deletion of the three 3'-most guanosines. |
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-Telomere-binding protein ... , 2 types, 2 molecules AB
#3: Protein | Mass: 52296.855 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 |
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#4: Protein | Mass: 24487.682 Da / Num. of mol.: 1 / Fragment: residues 9-224 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 |
-Non-polymers , 3 types, 508 molecules
#5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-CL / | #7: 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: 3.04 Å3/Da / Density % sol: 59.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 3.1→29.96 Å / Num. all: 21070 / Num. obs: 19176 |
Reflection | *PLUS % possible obs: 91.1 % / Rmerge(I) obs: 0.126 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→29.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 791551.1 / 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: 15.8035 Å2 / ksol: 0.275927 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→29.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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