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Yorodumi- PDB-2cqx: Solution structure of RSGI RUH-034, a homeodomain from mouse cDNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cqx | ||||||
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Title | Solution structure of RSGI RUH-034, a homeodomain from mouse cDNA | ||||||
Components | LAG1 longevity assurance homolog 5 | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Homeodomain / DNA binding domain / Transcription / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information sphingosine N-acyltransferase / sphingoid base N-palmitoyltransferase / Sphingolipid de novo biosynthesis / sphingosine N-acyltransferase activity / sphingolipid biosynthetic process / ceramide biosynthetic process / endoplasmic reticulum membrane / endoplasmic reticulum / DNA binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ruhul Momen, A.Z.M. / Onuki, H. / Hirota, H. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of RSGI RUH-034, a homeodomain from mouse cDNA Authors: Ruhul Momen, A.Z.M. / Onuki, H. / Hirota, H. / Tomizawa, T. / Koshiba, 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 | 2cqx.cif.gz | 438.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cqx.ent.gz | 367.6 KB | Display | PDB format |
PDBx/mmJSON format | 2cqx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cqx_validation.pdf.gz | 342.6 KB | Display | wwPDB validaton report |
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Full document | 2cqx_full_validation.pdf.gz | 487.5 KB | Display | |
Data in XML | 2cqx_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 2cqx_validation.cif.gz | 43.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/2cqx ftp://data.pdbj.org/pub/pdb/validation_reports/cq/2cqx | 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: 8046.037 Da / Num. of mol.: 1 / Fragment: residues 8-66 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free Protein Synthesis (E. coli) / Plasmid: P040727-13 / References: UniProt: Q9D6K9 |
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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: 1.30mM Domain U 15N, 13C; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM NaCl / 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 |