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Yorodumi- PDB-4ypl: Crystal structure of a hexameric LonA protease bound to three ADPs -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ypl | ||||||
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Title | Crystal structure of a hexameric LonA protease bound to three ADPs | ||||||
Components | Lon protease | ||||||
Keywords | HYDROLASE / Lon protease / ADP / MMH8709 / Inhibitor / AAA+ domain | ||||||
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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Meiothermus taiwanensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å | ||||||
Authors | Lin, C.-C. / Chang, C.-I. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ypl.cif.gz | 616.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ypl.ent.gz | 511.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ypl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ypl_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 4ypl_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 4ypl_validation.xml.gz | 139.1 KB | Display | |
Data in CIF | 4ypl_validation.cif.gz | 183.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/4ypl ftp://data.pdbj.org/pub/pdb/validation_reports/yp/4ypl | HTTPS FTP |
-Related structure data
Related structure data | 4ypnSC 1qzmS 1rr9S S: Starting model for refinement C: citing same article (ref.) |
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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: 61329.273 Da / Num. of mol.: 6 Fragment: AAA+ domain, protease domain, UNP residues 242-793 Mutation: E423Q 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: Chemical | ChemComp-4KZ / #3: Chemical | |
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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: 2.63 Å3/Da / Density % sol: 53.22 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 8.7 Details: 0.1 M Tris-HCl pH 8.7, 0.1 M CaCl2, 10-13% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.45→50 Å / Num. all: 52050 / Num. obs: 45968 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Net I/av σ(I): 13.22 / Net I/σ(I): 0.168 |
Reflection shell | Resolution: 3.45→3.47 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.53 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YPN, 1QZM and 1RR9 Resolution: 3.45→30 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.841 / Cross valid method: THROUGHOUT / ESU R Free: 0.706 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 66.574 Å2
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Refinement step | Cycle: LAST / Resolution: 3.45→30 Å
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Refine LS restraints |
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