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- PDB-1xjy: The crystal structures of the DNA binding sites of the RUNX1 tran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xjy | ||||||
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Title | The crystal structures of the DNA binding sites of the RUNX1 transcription factor | ||||||
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![]() | DNA / A-DNA / DOUBLE HELIX / OVERHANGING BASES / RUNX1 | ||||||
Function / homology | DNA![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z. | ||||||
![]() | ![]() Title: Structures of the DNA-binding site of Runt-domain transcription regulators. Authors: Kitayner, M. / Rozenberg, H. / Rabinovich, D. / Shakked, Z. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 20.3 KB | Display | ![]() |
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PDB format | ![]() | 12.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 382.9 KB | Display | ![]() |
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Full document | ![]() | 384.4 KB | Display | |
Data in XML | ![]() | 4 KB | Display | |
Data in CIF | ![]() | 5.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() | |||||||||
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: 2→19 Å / Num. obs: 2975 / % possible obs: 100 % / Redundancy: 7.1 % / Rsym value: 0.042 / Net I/σ(I): 52.4 | |||||||||
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 8.9 / Rsym value: 0.261 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: FIBER A-DNA Resolution: 2→15 Å / Num. parameters: 1696 / Num. restraintsaints: 5755 / 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: 420 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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