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Yorodumi- PDB-1ny6: Crystal structure of sigm54 activator (AAA+ ATPase) in the active... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ny6 | ||||||
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Title | Crystal structure of sigm54 activator (AAA+ ATPase) in the active state | ||||||
Components | transcriptional regulator (NtrC family) | ||||||
Keywords | TRANSCRIPTION / AAA+ ATPase / sigma54 activator / bacterial transcription / heptamer | ||||||
Function / homology | Function and homology information phosphorelay signal transduction system / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Lee, S.Y. / de la Torre, A. / Kustu, S. / Nixon, B.T. / Wemmer, D.E. | ||||||
Citation | Journal: Genes Dev. / Year: 2003 Title: Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains Authors: Lee, S.Y. / de la Torre, A. / Yan, D. / Kustu, S. / Nixon, B.T. / 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 | 1ny6.cif.gz | 683.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ny6.ent.gz | 565.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ny6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1ny6 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1ny6 | HTTPS FTP |
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-Related 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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Details | The biological assembly is a heptamer that forms a ring-like structure in the assymetric unit (there are 14 molecules in the assymetric unit) |
-Components
#1: Protein | Mass: 30618.445 Da / Num. of mol.: 14 / Fragment: residues 122-387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: NtrC1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: O67198 #2: Chemical | ChemComp-ADP / |
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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: 2.92 Å3/Da / Density % sol: 57.54 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: diammonium tartrate, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 17, 2002 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→62.02 Å / Num. obs: 86929 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 103 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.1→3.27 Å / % possible all: 97.1 |
Reflection shell | *PLUS % possible obs: 97.1 % / Rmerge(I) obs: 0.421 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.98 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.221601 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 103.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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