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Yorodumi- PDB-2dhk: Solution structure of the PH domain of TBC1 domain family member ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dhk | ||||||
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Title | Solution structure of the PH domain of TBC1 domain family member 2 protein from human | ||||||
Components | TBC1 domain family member 2 | ||||||
Keywords | IMMUNE SYSTEM / PH domain / PARIS-1 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information small GTPase binding => GO:0031267 / activation of GTPase activity / TBC/RABGAPs / GTPase activator activity / positive regulation of GTPase activity / intracellular protein transport / cell junction / cytoplasmic vesicle / cadherin binding / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Li, H. / Tochio, N. / Koshiba, S. / Harada, T. / Watanabe, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PH domain of TBC1 domain family member 2 protein from human Authors: Li, H. / Tochio, N. / Koshiba, S. / Harada, T. / Watanabe, S. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dhk.cif.gz | 715.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dhk.ent.gz | 601.8 KB | Display | PDB format |
PDBx/mmJSON format | 2dhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dhk_validation.pdf.gz | 345.2 KB | Display | wwPDB validaton report |
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Full document | 2dhk_full_validation.pdf.gz | 492.8 KB | Display | |
Data in XML | 2dhk_validation.xml.gz | 41 KB | Display | |
Data in CIF | 2dhk_validation.cif.gz | 63.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/2dhk ftp://data.pdbj.org/pub/pdb/validation_reports/dh/2dhk | 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: 13309.069 Da / Num. of mol.: 1 / Fragment: PH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TBC1D2, PARIS1 / Plasmid: P051205-24 / Production host: Cell free synthesis / References: UniProt: Q9BYX2 |
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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: 1.31mM PH domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 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: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 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 least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |