+Open data
-Basic information
Entry | Database: PDB / ID: 7l0i | ||||||
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Title | Ligand-free YopH G352T | ||||||
Components | Protein-tyrosine-phosphatase | ||||||
Keywords | HYDROLASE / Protein Tyrosine Phosphatase | ||||||
Function / homology | Function and homology information protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Shen, R.D. / Hengge, A.C. / Johnson, S.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Jacs Au / Year: 2021 Title: Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases. Authors: Shen, R. / Crean, R.M. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l0i.cif.gz | 124.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l0i.ent.gz | 93.7 KB | Display | PDB format |
PDBx/mmJSON format | 7l0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/7l0i ftp://data.pdbj.org/pub/pdb/validation_reports/l0/7l0i | HTTPS FTP |
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-Related structure data
Related structure data | 7l0cC 7l0hC 7l0mC 4yaaS 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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Unit cell |
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-Components
#1: Protein | Mass: 33597.938 Da / Num. of mol.: 1 / Mutation: G352T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) Gene: yopH, Y0013, YPCD1.67c, G4D65_20050, G4D67_19670, GD372_22270 Production host: Escherichia coli (E. coli) / References: UniProt: O68720, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-EPE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, and 15-34 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.02→50 Å / Num. obs: 17704 / % possible obs: 95.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.079 / Rrim(I) all: 0.198 / Χ2: 1.051 / Net I/σ(I): 7.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YAA Resolution: 2.02→49.17 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.74 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.37 Å2 / Biso mean: 34.9746 Å2 / Biso min: 22.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.02→49.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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