+Open data
-Basic information
Entry | Database: PDB / ID: 7dhd | ||||||
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Title | Vibrio vulnificus Wzb | ||||||
Components | Protein-tyrosine-phosphataseProtein tyrosine phosphatase | ||||||
Keywords | HYDROLASE / Vibrio / Wzb / low molecular weight protein tyrosine phosphatase (LMWPTP) / capsular polysaccharide | ||||||
Function / homology | Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase Function and homology information | ||||||
Biological species | Vibrio vulnificus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Ma, Q. / Wang, X. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dhd.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dhd.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 7dhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/7dhd ftp://data.pdbj.org/pub/pdb/validation_reports/dh/7dhd | HTTPS FTP |
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-Related structure data
Related structure data | 7dheC 7dhfC 2wmyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16314.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio vulnificus (bacteria) / Gene: wzb / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: E5F0S0, protein-tyrosine-phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Free VvWzb crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT) and 1.5 ul of reservoir solution (100 mM ...Details: Free VvWzb crystals were grown in drops containing 1.5 ul of protein solution (14 mg/ml in the buffer 10 mM HEPES pH 7.5, 150 mM NaCl, 1 mM DTT) and 1.5 ul of reservoir solution (100 mM HEPES pH7.5, 200 mM NaCl, 31% (w/v) PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å |
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: 1.71→58.66 Å / Num. obs: 29957 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Rsym value: 0.085 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.711→1.74 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1506 / CC1/2: 0.788 / Rpim(I) all: 0.343 / Rrim(I) all: 1.238 / Rsym value: 1.188 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2WMY Resolution: 1.71→58.66 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.133 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.111
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Displacement parameters | Biso max: 111.09 Å2 / Biso mean: 32.58 Å2 / Biso min: 15.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.71→58.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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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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