[English] 日本語
![](img/lk-miru.gif)
- PDB-5x21: Crystal structure of Thermus thermophilus transcription initiatio... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5x21 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM) | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA / Transcription / RNA polymerase / transcription inhibition / nucleoside-analog inhibitor / pseudouridimycin / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Ebright, R. | ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 729.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 584.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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.) ![]() ![]() ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() 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) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / References: UniProt: Q72ID6, DNA-directed RNA polymerase |
---|
-Promoter DNA ... , 2 types, 2 molecules GH
#6: DNA chain | Mass: 6464.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
---|---|
#7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-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.) ![]() ![]() Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: sigA, rpoD, TT_C0164 / Plasmid: pET28a / Production host: ![]() ![]() |
---|---|
#8: RNA chain | Mass: 629.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Non-polymers , 4 types, 44 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PUM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/PUM.gif)
![](data/chem/img/HOH.gif)
#9: Chemical | ChemComp-MG / #10: Chemical | #11: Chemical | ChemComp-PUM / ( | #12: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.23 % / Description: rod |
---|---|
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|