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Yorodumi- PDB-1x4z: Solution structure of the 2nd fibronectin type III domain from mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x4z | ||||||
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Title | Solution structure of the 2nd fibronectin type III domain from mouse biregional cell adhesion molecule-related/down-regulated oncogenes (Cdon) binding protein | ||||||
Components | biregional cell adhesion molecule-related/down-regulated oncogenes (Cdon)binding protein | ||||||
Keywords | CELL ADHESION / fibronectin type III / fn3 / immunoglobulin-like beta-sandwich fold / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information Activation of SMO / regulation of striated muscle tissue development / Myogenesis / cell projection organization / smoothened signaling pathway / positive regulation of myoblast differentiation / axonal growth cone / axon guidance / cell-cell adhesion / nervous system development ...Activation of SMO / regulation of striated muscle tissue development / Myogenesis / cell projection organization / smoothened signaling pathway / positive regulation of myoblast differentiation / axonal growth cone / axon guidance / cell-cell adhesion / nervous system development / growth cone / axon / neuronal cell body / cell surface / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Tomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the 2nd fibronectin type III domain from mouse biregional cell adhesion molecule-related/down-regulated oncogenes (Cdon) binding protein Authors: Tomizawa, T. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x4z.cif.gz | 698.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x4z.ent.gz | 585.9 KB | Display | PDB format |
PDBx/mmJSON format | 1x4z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x4z_validation.pdf.gz | 341.1 KB | Display | wwPDB validaton report |
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Full document | 1x4z_full_validation.pdf.gz | 471.4 KB | Display | |
Data in XML | 1x4z_validation.xml.gz | 38.8 KB | Display | |
Data in CIF | 1x4z_validation.cif.gz | 62.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x4/1x4z ftp://data.pdbj.org/pub/pdb/validation_reports/x4/1x4z | 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: 12820.342 Da / Num. of mol.: 1 / Fragment: fibronectin type III (fn3) domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: Boc / Plasmid: P040719-11 / References: UniProt: Q6KAM5, UniProt: Q6AZB0*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: 1.43mM fn3 domain U-15N,13C; 20mM d-Tris-HCl; 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 / pH: 7 / Pressure: ambient / Temperature: 296 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, restrained molecular 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 |