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Yorodumi- PDB-4fth: Crystal Structure of NtrC4 DNA-binding domain bound to double-str... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fth | ||||||
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Title | Crystal Structure of NtrC4 DNA-binding domain bound to double-stranded DNA | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATOR/DNA / sigma-54 / transcriptional activator / DNA-binding domain / NtrC / Fis / helix-turn-helix / DNA-binding / TRANSCRIPTION REGULATOR-DNA complex | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å | ||||||
Authors | Vidangos, N.K. / Heideker, J. / Lyubimov, A.Y. / Lamers, M. / Huo, Y. / Pelton, J.G. / Ton, J. / Gralla, J.D. / Kuriyan, J. / Berger, J.M. / Wemmer, D.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2014 Title: DNA Recognition by a sigma (54) Transcriptional Activator from Aquifex aeolicus. Authors: Vidangos, N.K. / Heideker, J. / Lyubimov, A. / Lamers, M. / Huo, Y. / Pelton, J.G. / Ton, J. / Gralla, J. / Berger, J. / Wemmer, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fth.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fth.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fth.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/4fth ftp://data.pdbj.org/pub/pdb/validation_reports/ft/4fth | HTTPS FTP |
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-Related structure data
Related structure data | 3e7lS 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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Unit cell |
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-Components
#1: Protein | Mass: 8441.859 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 374-442) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aq_164, ntrC4 / Plasmid: Rosetta.pLysS / Production host: Escherichia coli (E. coli) / References: UniProt: O66551 #2: DNA chain | | Mass: 6734.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: lpxC upstream DNA-binding site, forward strand #3: DNA chain | | Mass: 6461.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: lpxC upstream DNA-binding site, reverse strand #4: 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: 2.41 Å3/Da / Density % sol: 48.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 30 mM Na-cacodylate pH 6.0, 140 mM spermidine, 50 mM potassium thiocyanate, and 15% (poly)ethylene glycol mw 400, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2010 |
Radiation | Monochromator: Khozu double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.1 Å / Num. all: 5902 / Num. obs: 5777 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Highest resolution: 3 Å / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 15.5 / Num. unique all: 5902 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E7L Resolution: 3.004→48.108 Å / SU ML: 0.5 / σ(F): 1.35 / Phase error: 30.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.071 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.004→48.108 Å
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Refine LS restraints |
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LS refinement shell |
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