[English] 日本語
Yorodumi- PDB-2fj6: Solution NMR structure of the UPF0346 protein yozE from Bacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fj6 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution NMR structure of the UPF0346 protein yozE from Bacillus subtilis. Northeast Structural Genomics target SR391. | ||||||
Components | Hypothetical UPF0346 protein yozE | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / SR391 / AutoStructure / Northeast Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Protein of unknown function UPF0346 / YozE SAM-like / YozE SAM-like domain / YozE SAM-like superfamily / YozE SAM-like fold / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha / UPF0346 protein YozE Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | SOLUTION NMR / Noesy assignments using AutoStructure, dyana, xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints, restrained res, 3.7 of which long range. 208 dihedral angle constraints, 42 h-bond constraints. | ||||||
Authors | Rossi, P. / Acton, T.B. / Cunningham, K.E. / Ma, L.C. / Shetty, K. / Swapna, G.V.T. / Xiao, R. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution NMR structure of the UPF0346 protein yozE from Bacillus subtilis. Northeast Structural Genomics target SR391. Authors: Rossi, P. / Acton, T.B. / Cunningham, K.E. / Ma, L.C. / Shetty, K. / Swapna, G.V.T. / Xiao, R. / Montelione, G.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2fj6.cif.gz | 267.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2fj6.ent.gz | 221.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/2fj6 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/2fj6 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 9995.864 Da / Num. of mol.: 1 / Fragment: protein yozE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: yozE / Plasmid: SR391-21.1-ss / Production host: Escherichia coli (E. coli) / Strain (production host): BL21MGK / References: UniProt: O31864 |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||
NMR details | Text: Automated backbone assignement using AutoAssign, manual sidechain assignment. Completeness: 95.3% BB, 88.2% SC, and 100% stereospecific Methyl assignments. Dihe. constr. determined with Talos ...Text: Automated backbone assignement using AutoAssign, manual sidechain assignment. Completeness: 95.3% BB, 88.2% SC, and 100% stereospecific Methyl assignments. Dihe. constr. determined with Talos and Hyper. RPF scores for NOE data consistency: Recall=0.932, Precision=0.874, F-measure=0.902 final DP score=0.738. RMSD ordered residues: 0.5 all BB, 1.0 all heavy atoms. Raw Procheck: psi-phi=0.1, all=-0.2, MolProbity 16.16. N-term tag included. |
-Sample preparation
Details |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Sample conditions | Ionic strength: 100 mM NaCl / pH: 5.5 / Pressure: atmospheric atm / Temperature: 293 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
---|---|
Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: Noesy assignments using AutoStructure, dyana, xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints, restrained res, 3.7 of which long range. 208 ...Method: Noesy assignments using AutoStructure, dyana, xplor for simulated annealing with a total of 1096 NOE distances. An average of 16.6 constraints, restrained res, 3.7 of which long range. 208 dihedral angle constraints, 42 h-bond constraints. Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 56 / Conformers submitted total number: 10 |