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Yorodumi- PDB-1d1q: CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d1q | ||||||
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Title | CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) COMPLEXED WITH THE SUBSTRATE PNPP | ||||||
Components | TYROSINE PHOSPHATASE (E.C.3.1.3.48) | ||||||
Keywords | HYDROLASE / BETA-ALPHA-BETA | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | ||||||
Authors | Wang, S. / Tabernero, L. / Zhang, M. / Harms, E. / Van Etten, R.L. / Staufacher, C.V. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate. Authors: Wang, S. / Tabernero, L. / Zhang, M. / Harms, E. / Van Etten, R.L. / Stauffacher, C.V. #1: Journal: J.Biol.Chem. / Year: 1995 Title: Cloning and Characterization of a Saccharomyces cerevisiae Gene Encoding the Low Molecular Weight Protein-tyrosine Phosphatase Authors: Ostanin, K. / Pokalsky, C. / Wang, S. / Van Etten, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d1q.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d1q.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d1q ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d1q | HTTPS FTP |
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-Related 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: 18671.154 Da / Num. of mol.: 2 / Mutation: C13A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PET23A / Production host: Escherichia coli (E. coli) / References: UniProt: P40347, protein-tyrosine-phosphatase #2: Chemical | ChemComp-4NP / | #3: Chemical | ChemComp-PO4 / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Compound details | Inactive mutant of LTP1 that the nucleophile cysteine is mutated to alanine. | |
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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: 2.21 Å3/Da / Density % sol: 44.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3400, Bis-TRIS, sodium chloride para-nitrophenyl phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 10, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 32773 / Num. obs: 32773 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.242 / Num. unique all: 1835 / % possible all: 50.2 |
Reflection | *PLUS Num. measured all: 240634 |
Reflection shell | *PLUS % possible obs: 50.2 % / Mean I/σ(I) obs: 3.38 |
-Processing
Software |
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Refinement | Resolution: 1.7→12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: bulk solvent model used
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Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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