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Yorodumi- PDB-1xjx: The crystal structures of the DNA binding sites of the RUNX1 tran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xjx | ||||||
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Title | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | ||||||
Components |
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Keywords | DNA / A-DNA / DOUBLE HELIX / OVERHANGING BASES / RUNX1 | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structures of the DNA-binding site of Runt-domain transcription regulators. Authors: Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xjx.cif.gz | 20.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xjx.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/1xjx ftp://data.pdbj.org/pub/pdb/validation_reports/xj/1xjx | HTTPS FTP |
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-Related 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: 2722.784 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.92 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, magnesium chloride, sodium cacodylate acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 / Wavelength: 1.5418 Å | |||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MIRROR | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→18.4 Å / Num. obs: 4315 / % possible obs: 95.9 % / Redundancy: 3.3 % / Rsym value: 0.039 / Net I/σ(I): 39.3 | |||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.236 / % possible all: 78.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FIBER A-DNA Resolution: 1.7→15 Å / Num. parameters: 1744 / Num. restraintsaints: 5767 / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: L.CLOWNEY ET AL.,J.AM.CHEM.SOC.118(1996)509-518, A.GELBIN ET AL.,J.AM.CHEM.SOC.118(1996)519-529, G.PARKINSON ET AL.,ACTA CRYST.D52(1996)57-64 Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 432 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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