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Yorodumi- PDB-1c8c: CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c8c | ||||||
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Title | CRYSTAL STRUCTURES OF THE CHROMOSOMAL PROTEINS SSO7D/SAC7D BOUND TO DNA CONTAINING T-G MISMATCHED BASE PAIRS | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN / PROTEIN-DNA INTERACTION / PROTEIN STABILITY / HYPERTHERMOPHILE / ACHAEABACTERIA / ELECTROSTATICS / MOLECULAR MODELING / T-G MISMATCH / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Su, S. / Gao, Y.-G. / Robinson, H. / Liaw, Y.-C. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H.-J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs. Authors: Su, S. / Gao, Y.G. / Robinson, H. / Liaw, Y.C. / Edmondson, S.P. / Shriver, J.W. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c8c.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8c.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 1c8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8c ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8c | HTTPS FTP |
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-Related structure data
Related structure data | 1ca5C 1ca6C 1azpS S: Starting model for refinement 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: 2442.616 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | | Mass: 7236.563 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) 1617, #1616 Source: (natural) Sulfolobus solfataricus (archaea) / References: UniProt: P39476 #3: 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: 1.8 Å3/Da / Density % sol: 39 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.3MM SSO7D, 1.3MM DUPLEX DNA, 2.5 MM TRIS (PH 6.5), 2.5% PEG 400, EQUILIBRATED AGAINST 15% PEG 400 at pH 6.5, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→20 Å / Num. obs: 14498 / % possible obs: 89.1 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 1.45 Å / Lowest resolution: 1.52 Å / % possible obs: 63 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AZP Resolution: 1.45→8 Å / Cross valid method: THROUGHOUT / σ(F): 4
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Refinement step | Cycle: LAST / Resolution: 1.45→8 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS σ(F): 4 / % reflection Rfree: 5 % / Rfactor Rwork: 0.229 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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