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Open data
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Basic information
Entry | Database: PDB / ID: 7dhe | ||||||
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Title | Vibrio vulnificus Wzb in complex with benzylphosphonate | ||||||
![]() | Protein-tyrosine-phosphatase | ||||||
![]() | HYDROLASE / Vibrio / Wzb / low molecular weight protein tyrosine phosphatase (LMWPTP) / capsular polysaccharide | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ma, Q. / Wang, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Wzb of Vibrio vulnificus represents a new group of low-molecular-weight protein tyrosine phosphatases with a unique insertion in the W-loop. Authors: Wang, X. / Ma, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.9 KB | Display | ![]() |
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PDB format | ![]() | 195.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7dhdC ![]() 7dhfC ![]() 2wmyS 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16314.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-B85 / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Complex crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml protein in the buffer 10 mM HEPES, 30 mM benzylphophonate, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1.5 ul of ...Details: Complex crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml protein in the buffer 10 mM HEPES, 30 mM benzylphophonate, 150 mM NaCl, 1 mM DTT, pH 7.5) and 1.5 ul of reservoir solution (100 mM HEPES pH 7.0, 25% (w/v) PEG3350). |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 2.785→48.14 Å / Num. obs: 13744 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rpim(I) all: 0.029 / Rrim(I) all: 0.055 / Rsym value: 0.047 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.785→2.833 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 689 / CC1/2: 0.811 / Rpim(I) all: 0.345 / Rrim(I) all: 0.666 / Rsym value: 0.568 / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2WMY Resolution: 2.79→48.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.347
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Displacement parameters | Biso max: 192.39 Å2 / Biso mean: 91.92 Å2 / Biso min: 48.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.79→48.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→3.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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