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- PDB-6vjs: Escherichia coli RNA polymerase and ureidothiophene-2-carboxylic ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vjs | |||||||||
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Title | Escherichia coli RNA polymerase and ureidothiophene-2-carboxylic acid complex | |||||||||
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![]() | TRANSCRIPTION / RNA polymerase Transcription | |||||||||
Function / homology | ![]() sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Murakami, K.S. / Molodtsov, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus -Based Wound Infection Model in SKH1 Mice. Authors: Haupenthal, J. / Kautz, Y. / Elgaher, W.A.M. / Patzold, L. / Rohrig, T. / Laschke, M.W. / Tschernig, T. / Hirsch, A.K.H. / Molodtsov, V. / Murakami, K.S. / Hartmann, R.W. / Bischoff, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.5 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 339.4 KB | Display | ![]() |
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Full document | ![]() | 340.2 KB | Display | |
Data in XML | ![]() | 2.2 KB | Display | |
Data in CIF | ![]() | 64.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lk1S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABFGCHDIEJ
#1: Protein | Mass: 36558.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 150820.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A8V4, UniProt: P0A8V2*PLUS, DNA-directed RNA polymerase #3: Protein | Mass: 155366.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein | Mass: 10249.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A802, UniProt: P0A800*PLUS, DNA-directed RNA polymerase |
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-Protein , 1 types, 2 molecules XY
#5: Protein | Mass: 70352.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 7 molecules ![](data/chem/img/QZY.gif)
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#6: Chemical | ChemComp-QZY / | ||
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#7: Chemical | ChemComp-ZN / #8: Chemical | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 62.01 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Hepes-NaOH (pH 8), 0.2M CaAcetate, 15% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 4→50.09 Å / Num. obs: 99417 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 157.35 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1056 / Rrim(I) all: 0.998 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 4→4.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8696 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 9506 / CC1/2: 0.728 / CC star: 0.918 / Rrim(I) all: 0.9644 / % possible all: 96.49 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LK1 Resolution: 4.02→50.09 Å / SU ML: 0.6153 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6291 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 205.45 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.02→50.09 Å
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Refine LS restraints |
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LS refinement shell |
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