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Yorodumi- PDB-5ezk: RNA polymerase model placed by Molecular replacement into X-ray d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ezk | ||||||
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Title | RNA polymerase model placed by Molecular replacement into X-ray diffraction map of DNA-bound RNA Polymerase-Sigma 54 holoenzyme complex. | ||||||
Components |
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Keywords | TRANSFERASE / RNA Polymerase | ||||||
Function / homology | Function and homology information RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / DNA-directed RNA polymerase 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 / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / DNA-directed RNA polymerase complex / regulation of DNA-templated transcription elongation / transcription antitermination / cell motility / DNA-templated transcription initiation / 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 / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 8.5 Å | ||||||
Authors | Darbari, V.C. / Yang, Y. / Lu, D. / Zhang, N. / Glyde, R. / Wang, Y. / Murakami, K.S. / Buck, M. / Zhang, X. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Science / Year: 2015 Title: TRANSCRIPTION. Structures of the RNA polymerase- Sigma 54 reveal new and conserved regulatory strategies. Authors: Yang, Y. / Darbari, V.C. / Zhang, N. / Lu, D. / Glyde, R. / Wang, Y.P. / Winkelman, J.T. / Gourse, R.L. / Murakami, K.S. / Buck, M. / Zhang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ezk.cif.gz | 489.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ezk.ent.gz | 332.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ezk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/5ezk ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ezk | HTTPS FTP |
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-Related structure data
Related structure data | 5nwtC 4igc S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoA, Z4665, ECs4160 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A7Z6, UniProt: P0A7Z4*PLUS, DNA-directed RNA polymerase #2: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoB, Z5560, ECs4910 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A8V4, UniProt: P0A8V2*PLUS, DNA-directed RNA polymerase #3: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoC, Z5561, ECs4911 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A8T8, UniProt: P0A8T7*PLUS, DNA-directed RNA polymerase #4: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rpoZ, b3649, JW3624 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, DNA-directed RNA polymerase |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.58 Å3/Da / Density % sol: 73.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 8% PGA-LM, 300mM Ammonium Formate, 100mM Hepes / PH range: 7.0 - 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2012 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 8.5→143.89 Å / Num. obs: 9102 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.996 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.089 / Rsym value: 0.08 / Net I/av σ(I): 11.5 / Net I/σ(I): 8.4 / Num. measured all: 91452 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4IGC 4igc Resolution: 8.5→143.89 Å / Cor.coef. Fo:Fc: 0.609 / Cor.coef. Fo:Fc free: 0.584 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso max: 217.99 Å2 / Biso mean: 33.644 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: final / Resolution: 8.5→143.89 Å
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LS refinement shell | Highest resolution: 8.5 Å |