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Yorodumi- PDB-2l0k: NMR solution structure of a transcription factor SpoIIID in compl... -
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-Basic information
Entry | Database: PDB / ID: 2l0k | ||||||
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Title | NMR solution structure of a transcription factor SpoIIID in complex with DNA | ||||||
Components | Stage III sporulation protein D | ||||||
Keywords | TRANSCRIPTION / SpoIIID / NMR solution structure / DNA binding / Bacillus subtilis / Transcription factor | ||||||
Function / homology | Sporulation stage III, transcriptional regulator SpoIIID / Stage III sporulation protein D / Transcription regulator, HTH DeoR-type, conserved site / DeoR-type HTH domain signature. / sporulation resulting in formation of a cellular spore / DNA-binding transcription factor activity / DNA binding / Stage III sporulation protein D Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | fewest violations, model 1 | ||||||
Authors | Chen, B. / Himes, P. / Lu, Z. / Liu, A. / Yan, H. / Kroos, L. | ||||||
Citation | Journal: To be Published Title: Novel Mode of DNA Binding by Bacterial Transcription Factor SpoIIID Authors: Chen, B. / Himes, P. / Liu, Y. / Zhang, Y. / Lu, Z. / Liu, A. / Yan, H. / Kroos, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l0k.cif.gz | 686 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l0k.ent.gz | 612.1 KB | Display | PDB format |
PDBx/mmJSON format | 2l0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/2l0k ftp://data.pdbj.org/pub/pdb/validation_reports/l0/2l0k | HTTPS FTP |
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-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: 10825.518 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spoIIID, BSU36420 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / References: UniProt: P15281 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: SpoIIID is evolutionarily conserved in endospore-forming bacteria and it activates or represses many genes during sporulation of Bacillus subtilis. A SpoIIID monomer binds DNA with high ...Details: SpoIIID is evolutionarily conserved in endospore-forming bacteria and it activates or represses many genes during sporulation of Bacillus subtilis. A SpoIIID monomer binds DNA with high affinity and sequence specificity. SpoIIID has a helix-turn-helix domain with a novel C-terminal helical extension. The recognition helix of the helix-turn-helix domain interacts with the major groove of DNA and the C-terminal helical extension interacts with the adjacent minor groove of DNA. This novel and efficient mode of DNA binding might have evolved uniquely in endospore-forming bacteria to conserve biosynthetic capacity as resources dwindle during the starvation-induced sporulation process. | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 10 mM potassium phosphate-1, 100 mM sodium chloride-2, 15 mM sodium azide-3, 0.05 mM DSS-4, 5.5 M [U-100% 2H] D2O-5, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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