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Open data
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Basic information
Entry | Database: PDB / ID: 1qy6 | ||||||
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Title | Structue of V8 Protease from Staphylococcus aureus | ||||||
![]() | serine protease | ||||||
![]() | Protease / serine protease | ||||||
Function / homology | ![]() glutamyl endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prasad, L. / Leduc, Y. / Hayakawa, K. / Delbaere, L.T.J. | ||||||
![]() | ![]() Title: The structure of a universally employed enzyme: V8 protease from Staphylococcus aureus. Authors: Prasad, L. / Leduc, Y. / Hayakawa, K. / Delbaere, L.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.3 KB | Display | ![]() |
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PDB format | ![]() | 39 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 29675.689 Da / Num. of mol.: 1 / Fragment: V8 Protease / Source method: isolated from a natural source Source: (natural) ![]() Species: Staphylococcus aureus / Strain: Mu50 / ATCC 700699 / References: UniProt: Q99V45, glutamyl endopeptidase |
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#2: Chemical | ChemComp-K / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: PEG 5000 mme, KCl, HEPES, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 300 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Feb 24, 1998 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 109774 / Num. obs: 20095 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Rmerge(I) obs: 0.09 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible all: 76 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 40 Å / % possible obs: 92 % / Redundancy: 6.3 % / Num. measured all: 97623 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / % possible obs: 76.2 % / Redundancy: 4.7 % / Num. unique obs: 790 / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Simulate annealing and conjugate gradient minimization
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Displacement parameters | Biso mean: 18.8 Å2 | ||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 1.97 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.3 |