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Yorodumi- PDB-2dmy: Solution structure of DSRM domain in Spermatid perinuclear RNA-bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dmy | ||||||
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Title | Solution structure of DSRM domain in Spermatid perinuclear RNA-bind protein | ||||||
Components | Spermatid perinuclear RNA-binding protein | ||||||
Keywords | RNA BINDING PROTEIN / DSRM domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information mechanosensory behavior / multicellular organism development / manchette / spermatid development / double-stranded RNA binding / microtubule binding / single-stranded RNA binding / DNA binding / RNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kadirvel, S. / He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of DSRM domain in Spermatid perinuclear RNA-bind protein Authors: Kadirvel, S. / He, F. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Terada, 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 | 2dmy.cif.gz | 554.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmy.ent.gz | 466.2 KB | Display | PDB format |
PDBx/mmJSON format | 2dmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmy_validation.pdf.gz | 344.1 KB | Display | wwPDB validaton report |
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Full document | 2dmy_full_validation.pdf.gz | 472.3 KB | Display | |
Data in XML | 2dmy_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 2dmy_validation.cif.gz | 49 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmy ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmy | 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: 10120.540 Da / Num. of mol.: 1 / Fragment: DSRM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell free protein synthesis / Gene: STRBP / Plasmid: P051128-11 / Production host: Cell free synthesis / References: UniProt: Q9H7V1, UniProt: Q96SI9*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: 0.8mM U-15, 13C; 20mM phosphate buffer NA; 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: 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 |