[English] 日本語
Yorodumi- PDB-4ypn: Crystal structure of a LonA fragment containing the 3-helix bundl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ypn | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a LonA fragment containing the 3-helix bundle and the AAA-alpha/beta domain | |||||||||
Components | Lon proteaseLon protease family | |||||||||
Keywords | HYDROLASE / AAA+ domain / Helix-bundle / disordered | |||||||||
Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / cellular response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Meiothermus taiwanensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | |||||||||
Authors | Chang, C.-I. / Lin, C.-C. | |||||||||
Funding support | Taiwan, 2items
| |||||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Insights into the Allosteric Operation of the Lon AAA+ Protease Authors: Lin, C.-C. / Su, S.-C. / Su, M.-Y. / Liang, P.-H. / Feng, C.-C. / Wu, S.-H. / Chang, C.-I. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ypn.cif.gz | 114.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ypn.ent.gz | 87 KB | Display | PDB format |
PDBx/mmJSON format | 4ypn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/4ypn ftp://data.pdbj.org/pub/pdb/validation_reports/yp/4ypn | HTTPS FTP |
---|
-Related structure data
Related structure data | 4yplC 3m6aS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33571.477 Da / Num. of mol.: 1 Fragment: 3-Helix-bundle and alpha/beta subdomain, UNP residues 207-492 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meiothermus taiwanensis (bacteria) / Gene: lonA1, lon / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A059VAZ3, endopeptidase La |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.37 % |
---|---|
Crystal grow | Temperature: 295 K / Method: evaporation / pH: 5.5 / Details: 0.1 M sodium citrate pH 5.5, 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→50 Å / Num. all: 16502 / Num. obs: 15628 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.49 |
Reflection shell | Resolution: 2.07→2.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 4.62 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3M6A Resolution: 2.07→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.321 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.758 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.07→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|