+Open data
-Basic information
Entry | Database: PDB / ID: 1rr9 | ||||||
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Title | Catalytic domain of E.coli Lon protease | ||||||
Components | ATP-dependent protease LaEndopeptidase La | ||||||
Keywords | HYDROLASE / ATP-dependent protease / catalytic dyad Ser-Lys | ||||||
Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity ...endopeptidase La / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / response to X-ray / cellular response to heat / peptidase activity / response to heat / sequence-specific DNA binding / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / DNA binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Botos, I. / Melnikov, E.E. / Cherry, S. / Tropea, J.E. / Khalatova, A.G. / Dauter, Z. / Maurizi, M.R. / Rotanova, T.V. / Wlodawer, A. / Gustchina, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site Authors: Botos, I. / Melnikov, E.E. / Cherry, S. / Tropea, J.E. / Khalatova, A.G. / Rasulova, F. / Dauter, Z. / Maurizi, M.R. / Rotanova, T.V. / Wlodawer, A. / Gustchina, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rr9.cif.gz | 210.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rr9.ent.gz | 176.7 KB | Display | PDB format |
PDBx/mmJSON format | 1rr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/1rr9 ftp://data.pdbj.org/pub/pdb/validation_reports/rr/1rr9 | HTTPS FTP |
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-Related 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: 21366.500 Da / Num. of mol.: 6 / Fragment: proteolytic domain / Mutation: S679A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: LON, CAPR, DEG, MUC, LOPA, B0439, C0555 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A9M0, endopeptidase La #2: Chemical | ChemComp-SO4 / #3: 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: 2.05 Å3/Da / Density % sol: 40.06 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate, PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2002 / Details: mirrors |
Radiation | Monochromator: MSC/Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 58314 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 99.5 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 127371 |
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |