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Yorodumi- PDB-1z0c: Crystal Structure of A. fulgidus Lon proteolytic domain D508A mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 1z0c | ||||||
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Title | Crystal Structure of A. fulgidus Lon proteolytic domain D508A mutant | ||||||
Components | Putative protease La homolog type | ||||||
Keywords | HYDROLASE / ATP-DEPENDENT PROTEASE / CATALYTIC SER-LYS DYAD / B-type Lon | ||||||
Function / homology | Function and homology information ATP-dependent peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein catabolic process / serine-type endopeptidase activity / regulation of DNA-templated transcription / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Botos, I. / Melnikov, E.E. / Cherry, S. / Kozlov, S. / Makhovskaya, O.V. / Tropea, J.E. / Gustchina, A. / Rotanova, T.V. / Wlodawer, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Atomic-resolution Crystal Structure of the Proteolytic Domain of Archaeoglobus fulgidus Lon Reveals the Conformational Variability in the Active Sites of Lon Proteases Authors: Botos, I. / Melnikov, E.E. / Cherry, S. / Kozlov, S. / Makhovskaya, O.V. / Tropea, J.E. / Gustchina, A. / Rotanova, T.V. / Wlodawer, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Pathological crystallography: case studies of several unusual macromolecular crystals Authors: Dauter, Z. / Botos, I. / LaRonde-LeBlanc, N. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1z0c.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1z0c.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 1z0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/1z0c ftp://data.pdbj.org/pub/pdb/validation_reports/z0/1z0c | 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: 22074.475 Da / Num. of mol.: 1 / Fragment: proteolytic domain / Mutation: D508A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: pJT12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pRIL / References: UniProt: O29883, endopeptidase La |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 32.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 600, calcium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. all: 23366 / Num. obs: 23366 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.55→1.59 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.134 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.108 / ESU R Free: 0.11 / 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: 34.427 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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