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Yorodumi- PDB-1ku2: Crystal Structure of Thermus aquaticus RNA Polymerase Sigma Subun... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ku2 | ||||||
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Title | Crystal Structure of Thermus aquaticus RNA Polymerase Sigma Subunit Fragment Containing Regions 1.2 to 3.1 | ||||||
Components | sigma factor sigA | ||||||
Keywords | TRANSCRIPTION / helices | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-templated transcription initiation / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | ||||||
Authors | Campbell, E.A. / Muzzin, O. / Chlenov, M. / Sun, J.L. / Olson, C.A. / Weinman, O. / Trester-Zedlitz, M.L. / Darst, S.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2002 Title: Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Authors: Campbell, E.A. / Muzzin, O. / Chlenov, M. / Sun, J.L. / Olson, C.A. / Weinman, O. / Trester-Zedlitz, M.L. / Darst, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ku2.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ku2.ent.gz | 81.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ku2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ku2_validation.pdf.gz | 383 KB | Display | wwPDB validaton report |
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Full document | 1ku2_full_validation.pdf.gz | 400.7 KB | Display | |
Data in XML | 1ku2_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 1ku2_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/1ku2 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/1ku2 | 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
#1: Protein | Mass: 27614.887 Da / Num. of mol.: 2 / Fragment: residues 92-332 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: pET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9EZJ8 #2: Chemical | |
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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: 4.8 Å3/Da / Density % sol: 74.36 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: MOPS, ammonium sulfate, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22.5 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Sep 14, 2000 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 24238 / Num. obs: 23536 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 6.2 / % possible all: 96.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 97790 / Rmerge(I) obs: 0.037 |
Reflection shell | *PLUS % possible obs: 96.5 % / Rmerge(I) obs: 0.147 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.23 / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.23 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.00787 |