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- PDB-4kn7: X-ray crystal structure of the Escherichia coli RNA polymerase in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kn7 | ||||||
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Title | X-ray crystal structure of the Escherichia coli RNA polymerase in complex with Benzoxazinorifamycin-2c | ||||||
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![]() | TRANSFERASE/ANTIBIOTIC / transcription / DNA / RNA / TRANSFERASE-ANTIBIOTIC complex | ||||||
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 / 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 / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murakami, K.S. | ||||||
![]() | ![]() Title: X-ray Crystal Structures of the Escherichia coli RNA Polymerase in Complex with Benzoxazinorifamycins. Authors: Molodtsov, V. / Nawarathne, I.N. / Scharf, N.T. / Kirchhoff, P.D. / Showalter, H.D. / Garcia, G.A. / Murakami, K.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.4 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4kmuC ![]() 4kn4C ![]() 4igc C: citing same article ( 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.) ![]() ![]() ![]() ![]() #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.) ![]() ![]() ![]() ![]() |
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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, 8 molecules ![](data/chem/img/1RM.gif)
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![](data/chem/img/MG.gif)
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#6: Chemical | #7: Chemical | ChemComp-ZN / #8: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.19 Å3/Da / Density % sol: 61.44 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M HEPES-HCl, pH 7.0, 0.2 M calcium acetate, ~15% PEG400, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2012 |
Radiation | Monochromator: Horizontal focusing asymmetric cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 3.686→30 Å / Num. obs: 118179 / % possible obs: 93.1 % / Redundancy: 4.2 % / Net I/σ(I): 7.6 |
Reflection shell | Highest resolution: 3.686 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.4 / % possible all: 87.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4IGC ![]() 4igc Resolution: 3.686→29.877 Å / SU ML: 0.71 / σ(F): 1.35 / Phase error: 34.69 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.686→29.877 Å
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Refine LS restraints |
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LS refinement shell |
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