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- PDB-1pxv: The staphostatin-staphopain complex: a forward binding inhibitor ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pxv | ||||||
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Title | The staphostatin-staphopain complex: a forward binding inhibitor in complex with its target cysteine protease | ||||||
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![]() | HYDROLASE / cysteine protease inhibitor | ||||||
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. / Rzychon, M. / Oleksy, A. / Gruca, M. / Dubin, A. / Potempa, J. / Bochtler, M. | ||||||
![]() | ![]() 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. #1: ![]() Title: Staphostatins resemble lipocalins, not cystatins in fold. Authors: Rzychon, M. / Filipek, R. / Sabat, A. / Kosowska, K. / Dubin, A. / Potempa, J. / Bochtler, M. #2: ![]() 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. #3: ![]() Title: Identification of a novel maturation mechanism and restricted substrate specificity for the SspB cysteine protease of Staphylococcus aureus Authors: Massimi, I. / Park, E. / Rice, K. / Muller-Esterl, W. / Sauder, D. / McGavin, M.J. | ||||||
History |
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Remark 999 | SEQUENCE At the time of processing, there was no database sequence available for the proteins from ...SEQUENCE At the time of processing, there was no database sequence available for the proteins from Staphylococcus aureus, strain V8 that were crystallized here. The closest homologues with protein sequences in a database were from Staphylococcus aureus subsp. aureus MW2. The author claims that the residue conflicts between strain V8 and strain MW2 noted here are genuine, confirmed strain differences. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 143 KB | Display | ![]() |
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PDB format | ![]() | 110.9 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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2 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21062.078 Da / Num. of mol.: 2 / Mutation: C243A 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: 13074.622 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9EYW6, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GAI / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.61 % | |||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 2 M (NH4)2SO4 and 5% isopropanol, 100 mM guanidinium hydrochloride, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 294K | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting 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: MARRESEARCH / Detector: CCD / Date: Jan 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20.92 Å / Num. all: 72496 / Num. obs: 66436 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3959 / Rsym value: 0.182 / % possible all: 89.3 |
Reflection | *PLUS Num. obs: 64796 / % possible obs: 92 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CV8, 1NYC Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.263 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 1.8 Å / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.192 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |