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Yorodumi- PDB-5or5: NMR structure of the complex formed by an engineered region 2 of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5or5 | ||||||
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Title | NMR structure of the complex formed by an engineered region 2 of sigmaE in complex with GTAAAA | ||||||
Components |
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Keywords | TRANSCRIPTION / promoter melting / -10 element recognition / ECF sigma factor | ||||||
Function / homology | Function and homology information sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / negative regulation of DNA-templated transcription ...sigma factor antagonist complex / response to osmotic stress / response to temperature stimulus / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) Bacillus subtilis (bacteria) synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Campagne, S. / Vorholt, J.A. / Allain, F.H. | ||||||
Citation | Journal: Not published Title: Engineered promoter selectivity of an ECF sigma factor Authors: Campagne, S. / Vorholt, J.A. / Allain, F.H. #1: Journal: Nat. Struct. Mol. Biol. / Year: 2014 Title: Structural basis for -10 promoter element melting by environmentally induced sigma factors. Authors: Campagne, S. / Marsh, M.E. / Capitani, G. / Vorholt, J.A. / Allain, F.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5or5.cif.gz | 452.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5or5.ent.gz | 375.5 KB | Display | PDB format |
PDBx/mmJSON format | 5or5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5or5_validation.pdf.gz | 405.8 KB | Display | wwPDB validaton report |
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Full document | 5or5_full_validation.pdf.gz | 522.2 KB | Display | |
Data in XML | 5or5_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5or5_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/5or5 ftp://data.pdbj.org/pub/pdb/validation_reports/or/5or5 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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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: 10990.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Bacillus subtilis (bacteria) Strain: K12, 168 / Gene: rpoE, sigE, b2573, JW2557, sigW, ybbL, BSU01730 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AGB6, UniProt: Q45585 |
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#2: DNA chain | Mass: 1761.288 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 60 mM / Label: conditions / pH: 6.5 Not defined / Pressure: atmospheric atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 30 / Conformers submitted total number: 13 |