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Yorodumi- PDB-5x21: Crystal structure of Thermus thermophilus transcription initiatio... -
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-Basic information
Entry | Database: PDB / ID: 5x21 | ||||||
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Title | Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM) | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Transcription / RNA polymerase / transcription inhibition / nucleoside-analog inhibitor / pseudouridimycin / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.323 Å | ||||||
Authors | Zhang, Y. / Ebright, R. | ||||||
Citation | Journal: Cell / Year: 2017 Title: Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase. Authors: Maffioli, S.I. / Zhang, Y. / Degen, D. / Carzaniga, T. / Del Gatto, G. / Serina, S. / Monciardini, P. / Mazzetti, C. / Guglierame, P. / Candiani, G. / Chiriac, A.I. / Facchetti, G. / ...Authors: Maffioli, S.I. / Zhang, Y. / Degen, D. / Carzaniga, T. / Del Gatto, G. / Serina, S. / Monciardini, P. / Mazzetti, C. / Guglierame, P. / Candiani, G. / Chiriac, A.I. / Facchetti, G. / Kaltofen, P. / Sahl, H.G. / Deho, G. / Donadio, S. / Ebright, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x21.cif.gz | 729.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x21.ent.gz | 584.2 KB | Display | PDB format |
PDBx/mmJSON format | 5x21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x21_validation.pdf.gz | 855.6 KB | Display | wwPDB validaton report |
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Full document | 5x21_full_validation.pdf.gz | 887.8 KB | Display | |
Data in XML | 5x21_validation.xml.gz | 114.5 KB | Display | |
Data in CIF | 5x21_validation.cif.gz | 156.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/5x21 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x21 | HTTPS FTP |
-Related 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: 35056.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rpoA / Production host: Thermus thermophilus (bacteria) References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase #2: Protein | | Mass: 125436.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | | Mass: 170997.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase #4: Protein | | Mass: 11533.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72ID6, DNA-directed RNA polymerase |
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-Promoter DNA ... , 2 types, 2 molecules GH
#6: DNA chain | Mass: 6464.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
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#7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
-Protein / RNA chain , 2 types, 2 molecules FI
#5: Protein | Mass: 50739.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: sigA, rpoD, TT_C0164 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q72L95 |
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#8: RNA chain | Mass: 629.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
-Non-polymers , 4 types, 44 molecules
#9: Chemical | ChemComp-MG / #10: Chemical | #11: Chemical | ChemComp-PUM / ( | #12: Water | ChemComp-HOH / | |
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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: 3.17 Å3/Da / Density % sol: 61.23 % / Description: rod |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris-HCl, pH 8.4, 200 mM potassium chloride, 50 mM magnesium chloride, 9.5% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 2, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→40 Å / Num. obs: 76928 / % possible obs: 92 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.43 Å2 / Rmerge(I) obs: 0.138 / Χ2: 1.068 / Net I/av σ(I): 8.35 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.323→39.668 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.69 / 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 MODELf | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.323→39.668 Å
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Refine LS restraints |
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LS refinement shell |
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