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Yorodumi- PDB-2e6o: Solution structure of the HMG box domain from human HMG-box trans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e6o | ||||||
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Title | Solution structure of the HMG box domain from human HMG-box transcription factor 1 | ||||||
Components | HMG box-containing protein 1 | ||||||
Keywords | TRANSCRIPTION / CELL CYCLE / HMG-box domain / HMG box containing protein 1 / HMG-box transcription factor 1 / High mobility group box transcription factor 1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Wnt signaling pathway / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / Torsion angle dynamic | ||||||
Authors | Qin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the HMG box domain from human HMG-box transcription factor 1 Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e6o.cif.gz | 542.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e6o.ent.gz | 457.5 KB | Display | PDB format |
PDBx/mmJSON format | 2e6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e6o_validation.pdf.gz | 341.8 KB | Display | wwPDB validaton report |
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Full document | 2e6o_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 2e6o_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2e6o_validation.cif.gz | 39.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/2e6o ftp://data.pdbj.org/pub/pdb/validation_reports/e6/2e6o | 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: 9999.562 Da / Num. of mol.: 1 / Fragment: HMG-box Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: HBP1 / Plasmid: P060206-06 / References: UniProt: O60381 |
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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: 1.16mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10%D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: Torsion angle dynamic / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |