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Open data
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Basic information
Entry | Database: PDB / ID: 1smy | ||||||
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Title | Structural basis for transcription regulation by alarmone ppGpp | ||||||
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![]() | TRANSFERASE / RNA POLYMERASE HOLOENZYME / Guanosine-tetraphosphate / ppGpp / transcription regulation / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Artsimovitch, I. / Patlan, V. / Sekine, S. / Vassylyeva, M.N. / Hosaka, T. / Ochi, K. / Yokoyama, S. / Vassylyev, D.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Structural basis for transcription regulation by alarmone ppGpp Authors: Artsimovitch, I. / Patlan, V. / Sekine, S. / Vassylyeva, M.N. / Hosaka, T. / Ochi, K. / Yokoyama, S. / Vassylyev, D.G. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | 1.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 409.3 KB | Display | |
Data in CIF | ![]() | 610.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iw7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-DNA-directed RNA polymerase ... , 3 types, 8 molecules ABKLCMDN
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase #2: Protein | Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Protein , 2 types, 4 molecules EOFP
#4: Protein | Mass: 11521.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 48568.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 4 types, 9399 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/G4P.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/G4P.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ZN / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.71 Å3/Da / Density % sol: 73.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: MG FORMATE, PEG400, SPERMIDINE, TRIS HCL, pH 5.80, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→40 Å / Num. all: 427231 / Num. obs: 409145 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.12 |
Reflection shell | Resolution: 2.7→2.9 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.1 / % possible all: 92.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IW7 Resolution: 2.7→40 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: This is a twinned structure. The twinning operator is (H,K,L) -> (-H,-K,L) and the twinning fraction is 0.5. The R-FACTOR is 0.186 and the R-FREE is 0.266 when this twinning operator is used.
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Displacement parameters | Biso mean: 58.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.7 Å / Rfactor Rfree: 0.322 / Rfactor Rwork: 0.303 |