+Open data
-Basic information
Entry | Database: PDB / ID: 1smy | ||||||
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Title | Structural basis for transcription regulation by alarmone ppGpp | ||||||
Components |
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Keywords | TRANSFERASE / RNA POLYMERASE HOLOENZYME / Guanosine-tetraphosphate / ppGpp / transcription regulation / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Artsimovitch, I. / Patlan, V. / Sekine, S. / Vassylyeva, M.N. / Hosaka, T. / Ochi, K. / Yokoyama, S. / Vassylyev, D.G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2004 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1smy.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1smy.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 1smy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/1smy ftp://data.pdbj.org/pub/pdb/validation_reports/sm/1smy | HTTPS FTP |
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-Related structure data
Related structure data | 1iw7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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) Thermus thermophilus (bacteria) 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) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE8, DNA-directed RNA polymerase |
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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) Thermus thermophilus (bacteria) / References: UniProt: Q8RQE7*PLUS #5: Protein | Mass: 48568.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 4239959, UniProt: Q5SKW1*PLUS |
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-Non-polymers , 4 types, 9399 molecules
#6: Chemical | ChemComp-MG / #7: Chemical | ChemComp-ZN / #8: Chemical | #9: 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: 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1.02 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |