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Yorodumi- PDB-5nwt: Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Ho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nwt | |||||||||
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Title | Crystal Structure of Escherichia coli RNA polymerase - Sigma54 Holoenzyme complex | |||||||||
Components |
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Keywords | TRANSFERASE / Sigma 54 / RNA polymerase / Holoenzyme / Transcription | |||||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / 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-binding transcription activator activity / 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 / nucleotidyltransferase activity / 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 / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Klebsiella pneumoniae subsp. rhinoscleromatis SB3432 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.76 Å | |||||||||
Authors | Zhang, X. / Buck, M. / Darbari, V.C. / Yang, Y. / Zhang, N. / Lu, D. / Glyde, R. / Wang, Y. / Winkelman, J. / Gourse, R.L. / Murakami, K.S. | |||||||||
Citation | Journal: Science / Year: 2015 Title: TRANSCRIPTION. Structures of the RNA polymerase-Sigma54 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 | 5nwt.cif.gz | 640.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nwt.ent.gz | 473.9 KB | Display | PDB format |
PDBx/mmJSON format | 5nwt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nwt_validation.pdf.gz | 474.2 KB | Display | wwPDB validaton report |
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Full document | 5nwt_full_validation.pdf.gz | 487.1 KB | Display | |
Data in XML | 5nwt_validation.xml.gz | 109.3 KB | Display | |
Data in CIF | 5nwt_validation.cif.gz | 151.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/5nwt ftp://data.pdbj.org/pub/pdb/validation_reports/nw/5nwt | HTTPS FTP |
-Related structure data
Related structure data | 5ezkC 4yg2S 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
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: rpoA, pez, phs, sez, b3295, JW3257 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A7Z4, 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 (strain K12) (bacteria) Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A8V2, 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 (strain K12) (bacteria) Gene: rpoC, tabB, b3988, JW3951 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, 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 (strain K12) (bacteria) Gene: rpoZ, b3649, JW3624 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0A800, DNA-directed RNA polymerase |
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-Protein , 1 types, 1 molecules M
#5: Protein | Mass: 51172.637 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. rhinoscleromatis SB3432 (bacteria) Gene: rpoN, KPR_4804 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: R4YEY9 |
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-Non-polymers , 2 types, 3 molecules
#6: Chemical | #7: Chemical | ChemComp-MG / | |
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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: 3.48 Å3/Da / Density % sol: 64.63 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 9% PEG8000, 18% Ethylene glycol, 100mM Sodium HEPES/MOPS Buffer, 0.03M NaF, 0.03M NaBr, 0.03M NaI, 0-10mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2014 / Details: mirrors |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.76→29.78 Å / Num. obs: 59333 / % possible obs: 98.4 % / Redundancy: 8.3 % / Biso Wilson estimate: 142 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.031 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3.76→3.89 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5578 / CC1/2: 0.845 / Rpim(I) all: 0.356 / % possible all: 91.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YG2 Resolution: 3.76→195.28 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.858 / SU B: 0.01 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.741 / ESU R Free: 0.876 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 557.86 Å2 / Biso mean: 194.624 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 3.76→195.28 Å
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LS refinement shell | Resolution: 3.76→3.858 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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