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Yorodumi- PDB-1qz0: Crystal Structure of the Yersinia Pestis Phosphatase YopH in Comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qz0 | ||||||
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Title | Crystal Structure of the Yersinia Pestis Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / PHOSPHATASE / PTPASE / YOPH / DEPHOSPHORYLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
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: 1.5 Å | ||||||
Authors | Phan, J. / Lee, K. / Cherry, S. / Tropea, J.E. / Burke Jr, T.R. / Waugh, D.S. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: High-Resolution Structure of the Yersinia pestis Protein Tyrosine Phosphatase YopH in Complex with a Phosphotyrosyl Mimetic-Containing Hexapeptide Authors: Phan, J. / Lee, K. / Cherry, S. / Tropea, J.E. / Burke Jr, T.R. / Waugh, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qz0.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qz0.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/1qz0 ftp://data.pdbj.org/pub/pdb/validation_reports/qz/1qz0 | HTTPS FTP |
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-Related structure data
Related structure data | 1yptS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33553.883 Da / Num. of mol.: 2 / Fragment: Catalytic Domain, Residues 164-468 / Mutation: C235R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Plasmid: pZZ1089 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 16082755, UniProt: O68720*PLUS, protein-tyrosine-phosphatase #2: Protein/peptide | #3: Water | ChemComp-HOH / | |
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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: 2.25 Å3/Da / Density % sol: 45.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 3350, 100 mM HEPES, 100 mM NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97148 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002 / Details: Mirrors |
Radiation | Monochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97148 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→25 Å / Num. all: 87736 / Num. obs: 87736 / % possible obs: 68 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 1.9 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.038 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.7 / Num. unique all: 6162 / % possible all: 68 |
Reflection | *PLUS % possible obs: 89.3 % / Rmerge(I) obs: 0.038 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YPT Resolution: 1.5→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1.8 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.51 Å /
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