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Yorodumi- PDB-1jb7: DNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jb7 | ||||||
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Title | DNA G-Quartets in a 1.86 A Resolution Structure of an Oxytricha nova Telomeric Protein-DNA Complex | ||||||
Components |
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Keywords | DNA-BINDING PROTEIN/DNA / telomere-binding protein / DNA-protein interactions / DNA hydration / sodium ion / quadruplex 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: 1.86 Å | ||||||
Authors | Horvath, M.P. / Schultz, S.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex. Authors: Horvath, M.P. / Schultz, S.C. #1: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal Structure of the Oxytricha Nova Telomere End Binding Protein Complexed with Single Strand DNA Authors: Horvath, M.P. / Schweiker, V.L. / Bevilacqua, J.M. / Ruggles, J.A. / Schultz, S.C. #2: Journal: Structure / Year: 1994 Title: Refined Solution Structure of the Dimeric Quadruplex Formed from the Oxytricha Telomeric Oligonucleotide d(GGGGTTTTGGGG) Authors: Schultze, P. / Smith, F.W. / Feigon, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jb7.cif.gz | 191 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jb7.ent.gz | 147.7 KB | Display | PDB format |
PDBx/mmJSON format | 1jb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jb7_validation.pdf.gz | 458.8 KB | Display | wwPDB validaton report |
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Full document | 1jb7_full_validation.pdf.gz | 470.7 KB | Display | |
Data in XML | 1jb7_validation.xml.gz | 33 KB | Display | |
Data in CIF | 1jb7_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/1jb7 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/1jb7 | 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-DNA chain , 1 types, 3 molecules DGH
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: 3' terminal single strand DNA sequence of macronuclear telomeres |
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-Telomere-binding protein ... , 2 types, 2 molecules AB
#2: Protein | Mass: 56168.301 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 / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P29549 |
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#3: Protein | Mass: 28716.672 Da / Num. of mol.: 1 / Fragment: 28 kDa N-terminal core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sterkiella nova (eukaryote) / Gene: MAC-41A / Plasmid: pKKT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P16458 |
-Non-polymers , 3 types, 508 molecules
#4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 51.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 4000, ethylene glycol, sodium chloride, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 282K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 6 Details: 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: 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: May 1, 1999 / Details: Bent Conical SI Mirror (RH Coating) |
Radiation | Monochromator: Bent Cylindrical GE (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→20 Å / Num. all: 92896 / Num. obs: 92060 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.86→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8678 / % possible all: 95.6 |
Reflection | *PLUS Num. measured all: 903239 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OTC Resolution: 1.86→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 418030.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber Details: 'Molecular replacement' consisted of rigid-body refinement of the 2.8 A room-temperature structure. G-quartet linked DNA dimer was built into 2Fo-Fc and Fo-Fc electron density maps one ...Details: 'Molecular replacement' consisted of rigid-body refinement of the 2.8 A room-temperature structure. G-quartet linked DNA dimer was built into 2Fo-Fc and Fo-Fc electron density maps one nucleotide at a time so as to avoid preconceived notions of strand topology. Used maximum likelihood intensities target for refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.61 Å2 / ksol: 0.302 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.86→20 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: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.333 / % reflection Rfree: 9.8 % |