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- PDB-1omj: CRYSTAL STRUCTURE OF A PSYCHROPHILIC ALKALINE PROTEASE FROM PSEUD... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1omj | ||||||
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Title | CRYSTAL STRUCTURE OF A PSYCHROPHILIC ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18 | ||||||
![]() | SERRALYSIN | ||||||
![]() | HYDROLASE / BETA JELLY ROLL | ||||||
Function / homology | ![]() serralysin / extracellular matrix / metalloendopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ravaud, S. / Gouet, P. / Haser, R. / Aghajari, N. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 81.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 438.4 KB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 32.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1o0qC ![]() 1o0tC ![]() 1om6C ![]() 1om7C ![]() 1om8C ![]() 1kapS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48727.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.67 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / 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: ![]() ![]() ![]() | |||||||||
Detector | Type: THOMSON/PRINCETON / Detector: CCD / Date: Sep 5, 1997 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.38→13.6 Å / Num. obs: 17980 / % possible obs: 93.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.04 | |||||||||
Reflection shell | Resolution: 2.38→2.51 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 1661 / Rsym value: 0.128 / % possible all: 59 | |||||||||
Reflection | *PLUS Num. measured all: 32163 / Rmerge(I) obs: 0.04 | |||||||||
Reflection shell | *PLUS % possible obs: 59 % / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 7.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KAP Resolution: 2.38→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.38→50 Å
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Refine LS restraints |
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Software | *PLUS Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS |