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Yorodumi- PDB-1lyv: High-resolution structure of the catalytically inactive yersinia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lyv | ||||||
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Title | High-resolution structure of the catalytically inactive yersinia tyrosine phosphatase C403A mutant in complex with phosphate. | ||||||
Components | PROTEIN-TYROSINE PHOSPHATASE YOPH | ||||||
Keywords | HYDROLASE / toxin / tyrosine phosphatase / yersinia | ||||||
Function / homology | Function and homology information protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region Similarity search - Function | ||||||
Biological species | Yersinia enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / direct replacement / Resolution: 1.363 Å | ||||||
Authors | Evdokimov, A.G. / Waugh, D.S. / Routzahn, K. / Tropea, J. / Cherry, S. | ||||||
Citation | Journal: To be Published Title: High-resolution structure of the catalytically inactive yersinia tyrosine phosphatase C403A mutant in complex with phosphate. Authors: Evdokimov, A.G. / Waugh, D.S. / Routzahn, K. / Tropea, J. / Cherry, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lyv.cif.gz | 136.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lyv.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1lyv ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1lyv | HTTPS FTP |
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-Related structure data
Related structure data | 1hy5S S: Starting model for refinement |
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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: 33537.820 Da / Num. of mol.: 1 / Fragment: PTPase domain / Mutation: P163M,C235R,C403S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YopH / Plasmid: pZZ1090 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15273, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 18% PEG8000, 200 mM NaCl, TRIS, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2001 / Details: X9B |
Radiation | Monochromator: single crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.363→24.66 Å / Num. all: 55811 / Num. obs: 55811 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.35 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.0362 / Net I/σ(I): 50.7 |
Reflection shell | Resolution: 1.36→1.5 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 4.3 / Num. unique all: 14225 / Rsym value: 0.158 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: direct replacement Starting model: pdb entry 1HY5 Resolution: 1.363→25 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: conujugate-gradient least-squares
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Displacement parameters | Biso mean: 18.3 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.12 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.363→25 Å
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Refine LS restraints |
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