+Open data
-Basic information
Entry | Database: PDB / ID: 5ond | |||||||||
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Title | RfaH from Escherichia coli in complex with ops DNA | |||||||||
Components |
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Keywords | TRANSCRIPTION / operon-specific transcription factor / transformer protein / binding of single stranded DNA / translation activation | |||||||||
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 / transcription antitermination / positive regulation of translation / DNA binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Zuber, P.K. / Artsimovitch, I. / Roesch, P. / Knauer, S.H. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Elife / Year: 2018 Title: The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. Authors: Zuber, P.K. / Artsimovitch, I. / NandyMazumdar, M. / Liu, Z. / Nedialkov, Y. / Schweimer, K. / Rosch, P. / Knauer, S.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ond.cif.gz | 130.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ond.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ond.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/5ond ftp://data.pdbj.org/pub/pdb/validation_reports/on/5ond | HTTPS FTP |
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-Related structure data
Related structure data | 2ougS S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 18322.137 Da / Num. of mol.: 2 / Mutation: L162A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rfaH, hlyT, sfrB, b3842, JW3818 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AFW0 #2: DNA chain | Mass: 2771.822 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) #3: 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: 2.15 Å3/Da / Density % sol: 48.84 % / Description: parallelepipedic, thin |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: protein:DNA molar ratio: 1:1 reservoir solution: 21 %(w/v) PEG monomethyl ether 550, 44.4 mM HEPES (pH 7.0), 4 mM MgCl2; drops: 2ul protein/DNA solution + 2 ul reservoir solution |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2017 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.55 Å / Num. obs: 19931 / % possible obs: 97.3 % / Redundancy: 5.4 % / Rsym value: 0.063 / Net I/σ(I): 13.96 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.47 / Num. unique obs: 2633 / Rsym value: 0.429 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OUG Resolution: 2.1→41.542 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 32.04 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.542 Å
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Refine LS restraints |
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LS refinement shell |
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