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- PDB-4oio: Crystal structure of Thermus thermophilus pre-insertion substrate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oio | ||||||
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Title | Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation | ||||||
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![]() | TRANSCRIPTION / TRANSFERASE / de novo transcription initiation / substrate complex / transcription initiation / i site / i+1 site / RNA polymerase / DNA/RNA/NTP binding / polymerization of ribonucleotides / nucleoid | ||||||
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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y. / Ebright, R.H. / Arnold, E. | ||||||
![]() | ![]() Title: GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides. Authors: Zhang, Y. / Degen, D. / Ho, M.X. / Sineva, E. / Ebright, K.Y. / Ebright, Y.W. / Mekler, V. / Vahedian-Movahed, H. / Feng, Y. / Yin, R. / Tuske, S. / Irschik, H. / Jansen, R. / Maffioli, S. / ...Authors: Zhang, Y. / Degen, D. / Ho, M.X. / Sineva, E. / Ebright, K.Y. / Ebright, Y.W. / Mekler, V. / Vahedian-Movahed, H. / Feng, Y. / Yin, R. / Tuske, S. / Irschik, H. / Jansen, R. / Maffioli, S. / Donadio, S. / Arnold, E. / Ebright, R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 733.6 KB | Display | ![]() |
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PDB format | ![]() | 582.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 118.7 KB | Display | |
Data in CIF | ![]() | 162.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mq9C ![]() 4oinC ![]() 4oipC ![]() 4oiqC ![]() 4oirC ![]() 4g7hS 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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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 natural source / Source: (natural) ![]() ![]() #2: Protein | | Mass: 125436.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | | Mass: 170997.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | | Mass: 11533.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 50769.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 2 types, 2 molecules GH
#6: DNA chain | Mass: 6480.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: promoter DNA template strand |
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#7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: promoter DNA nontemplate strand |
-Non-polymers , 5 types, 221 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/2TM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/2TM.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | #9: Chemical | #10: Chemical | ChemComp-ATP / | #11: Chemical | ChemComp-2TM / | #12: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.94 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 100364 / Num. obs: 100364 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 59.22 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4976 / Rsym value: 1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4G7H Resolution: 3.1→48.919 Å / SU ML: 0.46 / Isotropic thermal model: ISOTROPIC TEMPERATURE FACTORS / σ(F): 1.34 / Phase error: 27.26 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→48.919 Å
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Refine LS restraints |
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LS refinement shell |
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