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Yorodumi- PDB-4qhg: Crystal structure of Methanocaldococcus jannaschii dimeric selecase -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qhg | ||||||
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Title | Crystal structure of Methanocaldococcus jannaschii dimeric selecase | ||||||
Components | Uncharacterized protein MJ1213 | ||||||
Keywords | HYDROLASE / Minigluzincin / Proteolytic enzyme | ||||||
Function / homology | Peptidase M56 / BlaR1 peptidase M56 / Uncharacterized protein MJ1213 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Lopez-pelegrin, M. / Cerda-costa, N. / Cintas-pedrola, A. / Herranz-trillo, F. / Bernado, P. / Peinado, J.R. / Arolas, J.L. / Gomis-ruth, F.X. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Multiple stable conformations account for reversible concentration-dependent oligomerization and autoinhibition of a metamorphic metallopeptidase Authors: Lopez-Pelegrin, M. / Cerda-Costa, N. / Cintas-Pedrola, A. / Herranz-Trillo, F. / Bernado, P. / Peinado, J.R. / Arolas, J.L. / Gomis-Ruth, F.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qhg.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qhg.ent.gz | 44.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qhg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qhg_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 4qhg_full_validation.pdf.gz | 436.7 KB | Display | |
Data in XML | 4qhg_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 4qhg_validation.cif.gz | 8.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/4qhg ftp://data.pdbj.org/pub/pdb/validation_reports/qh/4qhg | HTTPS FTP |
-Related structure data
Related structure data | 4qhfC 4qhhC 4qhiC 4qhjC 4jixS 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: 13103.546 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1213 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58610 | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 46.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M sodium cacodylate, 30%(v/v) 2-methyl-2,4-pentanediol, 3%(w/v) polyethylene glycol 8,000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→43.5 Å / Num. all: 6813 / Num. obs: 6813 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.2→43.5 Å / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 23.4 / Num. unique all: 6813 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JIX Resolution: 2.2→41.2 Å / Cor.coef. Fo:Fc: 0.9322 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 51.22 Å2
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Refine analyze | Luzzati coordinate error obs: 0.329 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→41.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.35 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: -1.1408 Å / Origin y: 0.8871 Å / Origin z: 18.3912 Å
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Refinement TLS group |
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