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- PDB-4zi4: YopH W354H Yersinia enterocolitica PTPase bond with Divanadate gl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zi4 | ||||||
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Title | YopH W354H Yersinia enterocolitica PTPase bond with Divanadate glycerol ester in the active site | ||||||
![]() | Tyrosine-protein phosphatase YopH | ||||||
![]() | HYDROLASE / phosphatase / Yersinia / PTP | ||||||
Function / homology | ![]() dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moise, G.E. / Johnson, S.J. / Hengge, A.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Conservative Tryptophan Mutants of the Protein Tyrosine Phosphatase YopH Exhibit Impaired WPD-Loop Function and Crystallize with Divanadate Esters in Their Active Sites. Authors: Moise, G. / Gallup, N.M. / Alexandrova, A.N. / Hengge, A.C. / Johnson, S.J. #1: ![]() Title: Locked WPD-loops and divanadate esters in two new tryptophan mutants of the protein-tyrosine phosphatase YopH Authors: Moise, G.E. / Johnson, S.J. / Hengge, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.3 KB | Display | ![]() |
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PDB format | ![]() | 147.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.9 KB | Display | ![]() |
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Full document | ![]() | 465.3 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yaaC ![]() 4z6bC ![]() 4zn5C ![]() 1yptS C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 33505.820 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP residues 164-468) / Mutation: C235R, W354H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-DVG / |
#3: Chemical | ChemComp-VO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Peg 3350, HEPES / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 98 K / Ambient temp details: under liquid nitrogen |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→50 Å / Num. obs: 109639 / % possible obs: 99.4 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 52.8 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 10.4 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YPT Resolution: 1.121→26.262 Å / FOM work R set: 0.931 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.844 Å2 / ksol: 0.413 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.97 Å2 / Biso mean: 20.01 Å2 / Biso min: 8.67 Å2
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Refinement step | Cycle: final / Resolution: 1.121→26.262 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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