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Yorodumi- PDB-1x63: Solution structure of the second LIM domain of skeletal muscle LI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x63 | ||||||
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Title | Solution structure of the second LIM domain of skeletal muscle LIM protein 1 | ||||||
Components | Skeletal muscle LIM-protein 1 | ||||||
Keywords | CONTRACTILE PROTEIN / LIM domain / Skeletal muscle LIM-protein 1 / Four and a half LIM domains protein 1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information negative regulation of G2/M transition of mitotic cell cycle / regulation of potassium ion transmembrane transporter activity / regulation of membrane depolarization / positive regulation of potassium ion transport / muscle organ development / negative regulation of G1/S transition of mitotic cell cycle / animal organ morphogenesis / negative regulation of cell growth / transmembrane transporter binding / cell differentiation ...negative regulation of G2/M transition of mitotic cell cycle / regulation of potassium ion transmembrane transporter activity / regulation of membrane depolarization / positive regulation of potassium ion transport / muscle organ development / negative regulation of G1/S transition of mitotic cell cycle / animal organ morphogenesis / negative regulation of cell growth / transmembrane transporter binding / cell differentiation / focal adhesion / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Nagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the second LIM domain of skeletal muscle LIM protein 1 Authors: Qin, X.R. / Nagashima, 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 | 1x63.cif.gz | 456.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x63.ent.gz | 379.6 KB | Display | PDB format |
PDBx/mmJSON format | 1x63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x63_validation.pdf.gz | 346.1 KB | Display | wwPDB validaton report |
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Full document | 1x63_full_validation.pdf.gz | 480.9 KB | Display | |
Data in XML | 1x63_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1x63_validation.cif.gz | 44.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x6/1x63 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/1x63 | 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: 8728.756 Da / Num. of mol.: 1 / Fragment: LIM domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: FHL1, SLIM1 / Plasmid: P040816-09 / References: UniProt: Q13642 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.24mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 0.01mM ZnCl2 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: 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 |