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Yorodumi- PDB-1se9: Structure of At3g01050, a ubiquitin-fold protein from Arabidopsis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1se9 | ||||||
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Title | Structure of At3g01050, a ubiquitin-fold protein from Arabidopsis thaliana | ||||||
Components | ubiquitin family | ||||||
Keywords | PLANT PROTEIN / ubiquitin-like / cell-free / wheat germ / Structural genomics / Protein structure Initiative / CESG / PSI / Center for Eukaryotic Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, cartesian molecular dynamics in explicit solvent | ||||||
Authors | Volkman, B.F. / Lytle, B.L. / Peterson, F.C. / Center for Eukaryotic Structural Genomics (CESG) | ||||||
Citation | Journal: Nat.Methods / Year: 2004 Title: Cell-free protein production and labeling protocol for NMR-based structural proteomics. Authors: Vinarov, D.A. / Lytle, B.L. / Peterson, F.C. / Tyler, E.M. / Volkman, B.F. / Markley, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1se9.cif.gz | 624.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1se9.ent.gz | 523.1 KB | Display | PDB format |
PDBx/mmJSON format | 1se9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1se9_validation.pdf.gz | 347.4 KB | Display | wwPDB validaton report |
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Full document | 1se9_full_validation.pdf.gz | 494.6 KB | Display | |
Data in XML | 1se9_validation.xml.gz | 29.7 KB | Display | |
Data in CIF | 1se9_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/1se9 ftp://data.pdbj.org/pub/pdb/validation_reports/se/1se9 | 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: 13970.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: At3g01050 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Description: WHEAT GERM CELL-FREE, IN VITRO EXPRESSION / Gene: At3g01050 / Plasmid: PEU-AT3G01050 / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9MAB9 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: Chemical shift assignments were obtained from standard 3D triple-resonance experiments, using the automated method of Garant (Christian Bartels). |
-Sample preparation
Details | Contents: 0.5 mM U-15N,13C At3g01050; 10mM phosphate buffer, 50mM KCl, 1mM DTT, pH 6.5 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM NaCl + 10 mM KPO4 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, cartesian molecular dynamics in explicit solvent Software ordinal: 1 Details: CANDID automated refinement Cyana refinement Xplor water refinement | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |