[English] 日本語
Yorodumi- PDB-1ny5: Crystal structure of sigm54 activator (AAA+ ATPase) in the inacti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ny5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of sigm54 activator (AAA+ ATPase) in the inactive state | ||||||
Components | transcriptional regulator (NtrC family) | ||||||
Keywords | TRANSCRIPTION / AAA+ ATPase / sigma54 activator / bacterial transcription / dimer | ||||||
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 / SAD / Resolution: 2.4 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ny5.cif.gz | 171 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ny5.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ny5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/1ny5 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/1ny5 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer in the assymetric unit (two molecules are in assymetric unit) |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44302.488 Da / Num. of mol.: 2 / Fragment: Regulatory and Central domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: NTRC1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O67198 |
---|
-Non-polymers , 5 types, 277 molecules
#2: Chemical | ChemComp-MG / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.06 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: sodium/potasium phosphate, citric acid,imidazole,methanol,glycerol,, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 40276 / Num. obs: 40276 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 35.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3 / % possible all: 83.4 |
Reflection | *PLUS Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 83.4 % / Rmerge(I) obs: 0.415 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.4→42.62 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.8258 Å2 / ksol: 0.348376 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.4 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.62 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 42.6 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|