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Open data
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Basic information
Entry | Database: PDB / ID: 1x9y | ||||||
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Title | The prostaphopain B structure | ||||||
![]() | cysteine proteinase![]() | ||||||
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Function / homology | ![]() cysteine-type peptidase activity / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Filipek, R. / Szczepanowski, R. / Sabat, A. / Potempa, J. / Bochtler, M. | ||||||
![]() | ![]() Title: Prostaphopain B structure: a comparison of proregion-mediated and staphostatin-mediated protease inhibition. Authors: Filipek, R. / Szczepanowski, R. / Sabat, A. / Potempa, J. / Bochtler, M. #1: ![]() Title: The Staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease. Authors: Filipek, R. / Rzychon, M. / Oleksy, A. / Gruca, M. / Dubin, A. / Potempa, J. / Bochtler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 281.3 KB | Display | ![]() |
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PDB format | ![]() | 228.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pxvS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Details | The protein is a monomer |
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Components
#1: Protein | ![]() Mass: 41846.504 Da / Num. of mol.: 4 / Fragment: proenzyme (residues 37-393) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q70UQ8, UniProt: P0C1S6*PLUS, ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.8 % |
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Crystal grow![]() | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 4000, 50 mM Bis-Tris, 5 mM Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 9, 2003 / Details: MSC Confocal MaxFlux mirrors |
Radiation | Monochromator: MSC Confocal MaxFlux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→20 Å / Num. all: 53566 / Num. obs: 53566 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3 / Num. unique all: 2535 / Rsym value: 0.339 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1PXV Resolution: 2.5→19.86 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2479432.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 24.0088 Å2 / ksol: 0.311264 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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