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Yorodumi- PDB-2dmt: Solution structure of the homeobox domain of Homeobox protein Bar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmt | ||||||
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Title | Solution structure of the homeobox domain of Homeobox protein BarH-like 1 | ||||||
Components | Homeobox protein BarH-like 1 | ||||||
Keywords | DNA BINDING PROTEIN / homeobox domain / three helices with the DNA binding helix-turn-helix motif / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information digestive system development / endothelial cell differentiation / anterior/posterior pattern specification / negative regulation of Wnt signaling pathway / spleen development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Wnt signaling pathway / cell-cell signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity ...digestive system development / endothelial cell differentiation / anterior/posterior pattern specification / negative regulation of Wnt signaling pathway / spleen development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Wnt signaling pathway / cell-cell signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ohnishi, S. / Yoneyama, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the homeobox domain of Homeobox protein BarH-like 1 Authors: Ohnishi, S. / Yoneyama, M. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dmt.cif.gz | 494.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmt.ent.gz | 416.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmt_validation.pdf.gz | 340.1 KB | Display | wwPDB validaton report |
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Full document | 2dmt_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 2dmt_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 2dmt_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmt ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmt | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8980.239 Da / Num. of mol.: 1 / Fragment: homeobox domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: BARX1 / Plasmid: P050919-24 / Production host: Cell free synthesis / References: UniProt: Q9HBU1 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0mM protein U-15N, 13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |