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Yorodumi- PDB-1d1p: CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d1p | ||||||
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Title | CRYSTAL STRUCTURE OF A YEAST LOW MOLECULAR WEIGHT PROTEIN TYROSINE PHOSPHATASE (LTP1) | ||||||
Components | TYROSINE PHOSPHATASE | ||||||
Keywords | HYDROLASE / BETA-ALPHA-BETA / TYROSINE PHOSPHATASE / LTP1 | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wang, S. / Tabernero, L. / Zhang, M. / Harms, E. / Van Etten, R.L. / Stauffacher, 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 | 1d1p.cif.gz | 78.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d1p.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 1d1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d1p_validation.pdf.gz | 448.7 KB | Display | wwPDB validaton report |
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Full document | 1d1p_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 1d1p_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1d1p_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d1p ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d1p | HTTPS FTP |
-Related structure data
Related structure data | 1d1qC 1pntS C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.156013, -0.737096, -0.657533), Vector: |
-Components
#1: Protein | Mass: 18572.025 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: P40347, protein-tyrosine-phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.8 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3400, HEPES, sodium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 12, 1995 / Details: double focussing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 15614 / Num. obs: 15614 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 7.28 / Num. unique all: 1414 / Rsym value: 0.204 / % possible all: 84.6 |
Reflection | *PLUS Num. measured all: 140622 |
Reflection shell | *PLUS % possible obs: 84.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Bovine low molecular weight protein tyrosine phosphatase (BPTP) PDB ID: 1PNT Resolution: 2.2→12 Å / Rfactor Rfree error: 0.007 / 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: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / 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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