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Yorodumi- PDB-2oug: Crystal structure of the RfaH transcription factor at 2.1A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oug | ||||||
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Title | Crystal structure of the RfaH transcription factor at 2.1A resolution | ||||||
Components | Transcriptional activator rfaH | ||||||
Keywords | TRANSCRIPTION / transcription factor / virulence / transcription pausing / transcription elongation | ||||||
Function / homology | Function and homology information regulatory RNA binding / transcription antitermination factor activity, DNA binding / translation activator activity / DNA-templated transcription elongation / bacterial-type RNA polymerase core enzyme binding / transcription elongation-coupled chromatin remodeling / positive regulation of translation / transcription antitermination / DNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Vassylyev, D.G. / Vassylyeva, M.N. / Svetlov, V. / Artsimovitch, I. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Authors: Belogurov, G.A. / Vassylyeva, M.N. / Svetlov, V. / Klyuyev, S. / Grishin, N.V. / Vassylyev, D.G. / Artsimovitch, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oug.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oug.ent.gz | 105.1 KB | Display | PDB format |
PDBx/mmJSON format | 2oug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/2oug ftp://data.pdbj.org/pub/pdb/validation_reports/ou/2oug | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Details | The biological assembly is a monomer |
-Components
#1: Protein | Mass: 18364.217 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaH, hlyT, sfrB / Plasmid: pVS12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (lambdaDE3) / References: UniProt: P0AFW0 #2: 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: 2.4 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG MME 5000, 50mM sodium cacodylate, 20 mM Co chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2005 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 38387 / Num. obs: 38387 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3238 / Rsym value: 0.497 / % possible all: 76.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED ...Details: THE PERFECT MEROHEDRAL TWINNING WAS DETECTED IN THE CRYSTALS WITH THE TWINNING OPERATOR {H,-H,-K,-L}. THE REFINEMENT STATISTICS PRESENTED FOR THIS ENTRY CORRESPONDS TO THE REFINEMENT CARRIED OUT USING THE TWINNING OPTION OF THE CNS PROGRAM. FOR THE DEPOSITION THE DIFFRACTION DATA WERE DETWINNED USING THE CNS PROGRAM. THEREFORE, SOME REFLECTIONS WERE LOST DUE TO THE DETWINNING PROCEDURE AND ARE MISSING IN THE DEPOSITED SF FILE, WHEREAS THE REFINEMENT STATISTICS CALCULATED BASED ON THE DETWINNED DATA MIGHT BE SLIGHTLY DIFFERENT FROM THOSE OBTAINED DURING THE "TWINNED" REFINEMENT INCLUDED IN THIS ENTRY.
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Displacement parameters | Biso mean: 43.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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