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- PDB-3bm8: crystal structure of YopH mutant D356A complexed with irreversibl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bm8 | ||||||
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Title | crystal structure of YopH mutant D356A complexed with irreversible inhibitor PVSN | ||||||
![]() | Tyrosine-protein phosphatase yopH | ||||||
![]() | HYDROLASE / co-valent binding / PVSN / binding selectivity / binding affinity / Membrane / Outer membrane / Plasmid / Protein phosphatase / Secreted / Virulence | ||||||
Function / homology | ![]() dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Z.Y. / Liu, S.J. | ||||||
![]() | ![]() Title: Aryl vinyl sulfonates and sulfones as active site-directed and mechanism-based probes for protein tyrosine phosphatases. Authors: Liu, S. / Zhou, B. / Yang, H. / He, Y. / Jiang, Z.X. / Kumar, S. / Wu, L. / Zhang, Z.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.8 KB | Display | ![]() |
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PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 387.3 KB | Display | ![]() |
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Full document | ![]() | 399.5 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bltC ![]() 3bluC ![]() 1pa9S 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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Unit cell |
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Components
#1: Protein | Mass: 33378.676 Da / Num. of mol.: 1 / Fragment: YopH catalytic domain / Mutation: C235R, D356A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PSY / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 25% PEG3350, 100 mM NaCl, 100 mM HEPES, pH7.0-8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 6365 / % possible obs: 86.1 % / Rmerge(I) obs: 0.098 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1pa9 Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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