+Open data
-Basic information
Entry | Database: PDB / ID: 4eti | ||||||
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Title | Crystal Structure of YwlE from Bacillus subtilis | ||||||
Components | Low molecular weight protein-tyrosine-phosphatase ywlE | ||||||
Keywords | HYDROLASE / Phosphatase / Dephosphorylation | ||||||
Function / homology | Function and homology information protein arginine phosphatase / protein arginine phosphatase activity / protein tyrosine phosphatase activity Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Cao, X.F. / Brostromer, E. / Liu, X.Y. / Su, X.D. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal Structure of YwlE from Bacillus subtilis Authors: Cao, X.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eti.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eti.ent.gz | 55.8 KB | Display | PDB format |
PDBx/mmJSON format | 4eti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/4eti ftp://data.pdbj.org/pub/pdb/validation_reports/et/4eti | HTTPS FTP |
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-Related structure data
Related structure data | 1zggS 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: 20363.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ywlE, BSU36930, ipc-31d / Production host: Escherichia coli (E. coli) / References: UniProt: P39155, protein-tyrosine-phosphatase |
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#2: Chemical | ChemComp-FMT / |
#3: 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: 1.7 Å3/Da / Density % sol: 26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M HCOONa, 20% PEG 3350, 0.1M spermidine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2005 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19 Å / Num. obs: 11539 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZGG Resolution: 1.8→18.917 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 19.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.762 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→18.917 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Origin x: -12.4094 Å / Origin y: -8.0651 Å / Origin z: -7.9117 Å
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Refinement TLS group | Selection details: CHAIN A |