+
Open data
-
Basic information
Entry | Database: PDB / ID: 1y4h | ||||||
---|---|---|---|---|---|---|---|
Title | Wild type staphopain-staphostatin complex | ||||||
![]() |
| ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / cysteine protease / inhibitor / staphopain B / staphostatin B / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() cysteine-type endopeptidase inhibitor activity / cysteine-type peptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Filipek, R. / Potempa, J. / Bochtler, M. | ||||||
![]() | ![]() Title: A comparison of staphostatin B with standard mechanism serine protease inhibitors. Authors: Filipek, R. / 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. #2: ![]() Title: Staphostatins resemble lipocalins, not cystatins in fold. Authors: Rzychon, M. / Filipek, R. / Sabat, A. / Kosowska, K. / Dubin, A. / Potempa, J. / Bochtler, M. #3: ![]() Title: Staphostatins: an expanding new group of proteinase inhibitors with a unique specificity for the regulation of staphopains, Staphylococcus spp. cysteine proteinases. Authors: Rzychon, M. / Sabat, A. / Kosowska, K. / Potempa, J. / Dubin, A. #4: ![]() 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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 471.1 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 32.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pxvS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 21550.619 Da / Num. of mol.: 2 / Fragment: residues 220-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q70UQ8, UniProt: P0C1S6*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Protein | Mass: 12930.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
---|---|
Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: 2M (NH4)2SO4, 9% isopropanol , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 21, 2004 / Details: MONOCHROMATIC |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→20 Å / Num. all: 53525 / Num. obs: 53525 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 30 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2087 / Rsym value: 0.32 / % possible all: 99.8 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PXV Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.608 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.903 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.93→1.98 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|