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- PDB-1qz0: Crystal Structure of the Yersinia Pestis Phosphatase YopH in Comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qz0 | ||||||
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Title | Crystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide | ||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / PHOSPHATASE / PTPASE / YOPH / DEPHOSPHORYLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Phan, J. / Lee, K. / Cherry, S. / Tropea, J.E. / Burke Jr, T.R. / Waugh, D.S. | ||||||
![]() | ![]() Title: High-Resolution Structure of the Yersinia pestis Protein Tyrosine Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide Authors: Phan, J. / Lee, K. / Cherry, S. / Tropea, J.E. / Burke Jr, T.R. / Waugh, D.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.6 KB | Display | ![]() |
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PDB format | ![]() | 106.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.6 KB | Display | ![]() |
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Full document | ![]() | 471.7 KB | Display | |
Data in XML | ![]() | 29.4 KB | Display | |
Data in CIF | ![]() | 44.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yptS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33553.883 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, Residues 164-468 / Mutation: C235R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 16082755, UniProt: O68720*PLUS, protein-tyrosine-phosphatase #2: Protein/peptide | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 100 mM HEPES, 100 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging 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: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002 / Details: Mirrors |
Radiation | Monochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97148 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. all: 87736 / Num. obs: 87736 / % possible obs: 68 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 1.9 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.038 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6162 / % possible all: 68 |
Reflection | *PLUS % possible obs: 89.3 % / Rmerge(I) obs: 0.038 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YPT Resolution: 1.5→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.8 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.51 Å /
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