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Yorodumi- PDB-2d8h: Solution structure of the SH3 domain of Hypothetical protein SH3YL1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2d8h | ||||||
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Title | Solution structure of the SH3 domain of Hypothetical protein SH3YL1 | ||||||
Components | SH3YL1 protein | ||||||
Keywords | UNKNOWN FUNCTION / SH3 domain / Hypothetical protein SH3YL1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of ruffle assembly / phosphatidylinositol biosynthetic process / phosphatase binding / phosphatidylinositol binding / ruffle membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Nagasima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be published Title: Solution structure of the SH3 domain of Hypothetical protein SH3YL1 Authors: Qin, X.R. / Nagasima, T. / 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 | 2d8h.cif.gz | 453.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d8h.ent.gz | 380.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d8h_validation.pdf.gz | 342.6 KB | Display | wwPDB validaton report |
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Full document | 2d8h_full_validation.pdf.gz | 456 KB | Display | |
Data in XML | 2d8h_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 2d8h_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/2d8h ftp://data.pdbj.org/pub/pdb/validation_reports/d8/2d8h | 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: 8595.269 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: SH3YL1 / Plasmid: P050425-18 / References: GenBank: 14249975, UniProt: Q96HL8*PLUS |
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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: 1.19mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3 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: 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 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 |