[English] 日本語
Yorodumi- PDB-1om7: CRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1om7 | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A COLD ADAPTED ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18, SOAKED IN 85 mM EDTA | ||||||
Components | SERRALYSIN | ||||||
Keywords | HYDROLASE / BETA JELLY ROLL | ||||||
Function / homology | Function and homology information serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. 'TAC II 18' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å | ||||||
Authors | Ravaud, S. / Gouet, P. / Haser, R. / Aghajari, N. | ||||||
Citation | Journal: J.Bacteriol. / Year: 2003 Title: Probing the role of divalent metal ions in a bacterial psychrophilic metalloprotease: binding studies of an enzyme in the crystalline state by x-ray crystallography. Authors: Ravaud, S. / Gouet, P. / Haser, R. / Aghajari, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1om7.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1om7.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1om7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/1om7 ftp://data.pdbj.org/pub/pdb/validation_reports/om/1om7 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 48727.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas sp. 'TAC II 18' (bacteria) / Strain: TAC II 18 / References: UniProt: O69771, serralysin | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.47 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium sulphate, Hepes, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop / Details: Villeret, V., (1997) Protein Sci., 6, 2462. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 4, 2002 / Details: MIRRORS |
Radiation | Monochromator: 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: 2.8→34.5 Å / Num. all: 11343 / Num. obs: 11326 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 36.66 Å2 / Rsym value: 0.147 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2 % / Rsym value: 0.249 / % possible all: 99.3 |
Reflection | *PLUS Num. measured all: 22739 / Rmerge(I) obs: 0.147 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.7 |
-Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→50 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
| |||||||||||||||||||||
Refine LS restraints |
|