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Yorodumi- PDB-2k6x: Autoregulation of a Group 1 Bacterial Sigma Factor Involves the F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k6x | ||||||
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Title | Autoregulation of a Group 1 Bacterial Sigma Factor Involves the Formation of a Region 1.1- Induced Compacted Structure | ||||||
Components | RNA polymerase sigma factor rpoD | ||||||
Keywords | TRANSCRIPTION / sigma 1.1 / DNA-binding / Sigma factor / Transcription regulation | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Authors | Schwartz, E.C. / Shekhtman, A. / Dutta, K. / Pratt, M.R. / Cowburn, D. / Darst, S. / Muir, T.W. | ||||||
Citation | Journal: Chem.Biol. / Year: 2008 Title: Autoregulation of a Group 1 Bacterial Sigma Factor Involves the Formation of a Region 1.1 - Induced Compacted Structure Authors: Schwartz, E.C. / Shekhtman, A. / Dutta, K. / Pratt, M.R. / Cowburn, D. / Darst, S. / Muir, T.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k6x.cif.gz | 448.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k6x.ent.gz | 376.1 KB | Display | PDB format |
PDBx/mmJSON format | 2k6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k6x_validation.pdf.gz | 341.8 KB | Display | wwPDB validaton report |
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Full document | 2k6x_full_validation.pdf.gz | 499.8 KB | Display | |
Data in XML | 2k6x_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 2k6x_validation.cif.gz | 44 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/2k6x ftp://data.pdbj.org/pub/pdb/validation_reports/k6/2k6x | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8336.333 Da / Num. of mol.: 1 / Fragment: UNP residues 29-96 / Mutation: S96G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: rpoD, sigA, TM_1451 / Production host: Escherichia coli (E. coli) / References: UniProt: P77994 |
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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: 300-800 uM [U-100% 15N] sigma1.1, 300-800 uM [U-100% 13C; U-100% 15N] sigma1.1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software | Name: CNS / Developer: Brunger A. T. et.al. / Classification: refinement |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 Details: Used Aria2.1, Intensities were converted into distance restraints using the symmetry ambiguous distance restraints (ADR) protocol |
NMR constraints | Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 53 |
NMR representative | Selection criteria: fewest violations |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 512 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å |
NMR ensemble rms | Distance rms dev: 0 Å |