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Yorodumi- PDB-2eh9: Crystal structure of the HBAF250B at-rich interaction domain (ARID) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2eh9 | ||||||
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Title | Crystal structure of the HBAF250B at-rich interaction domain (ARID) | ||||||
Components | AT-rich interactive domain-containing protein 1B | ||||||
Keywords | DNA BINDING PROTEIN / DNA-BINDING DOMAIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / cellular response to angiotensin / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair ...bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / cellular response to angiotensin / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / transcription initiation-coupled chromatin remodeling / response to ischemia / positive regulation of cell differentiation / RMTs methylate histone arginines / nervous system development / transcription coactivator activity / chromatin remodeling / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Niwa, H. / Shimada, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the HBAF250B at-rich interaction domain (ARID) Authors: Shimada, A. / Niwa, H. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eh9.cif.gz | 37 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eh9.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 2eh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eh/2eh9 ftp://data.pdbj.org/pub/pdb/validation_reports/eh/2eh9 | HTTPS FTP |
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-Related structure data
Related structure data | 2cxyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13973.688 Da / Num. of mol.: 1 / Fragment: AT-RICH INTERACTION DOMAIN (ARID) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: CELL-FREE PROTEIN SYNTHESIS / Gene: HBAF250B / Plasmid: PX041105-20 / References: UniProt: Q8NFD5 | ||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | #4: 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: 2.38 Å3/Da / Density % sol: 48.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: DNA(dCGCGAATTCGCG), 120MM MGCL2, 60MM TRIS-HCL, 18% PEG4000, 20MM ZNCL2, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 27, 2005 |
Radiation | Monochromator: SI DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 9616 / Num. obs: 9616 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 36.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.7 / Num. unique all: 767 / % possible all: 81.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CXY Resolution: 2→36.89 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1252250.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.5711 Å2 / ksol: 0.374269 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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