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Yorodumi- PDB-4kk4: YwlE arginine phosphatase - C7S mutant with phosphorylated active... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kk4 | ||||||
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Title | YwlE arginine phosphatase - C7S mutant with phosphorylated active site serine | ||||||
Components | Low molecular weight protein-tyrosine-phosphatase YwlE | ||||||
Keywords | HYDROLASE / protein modification / arginine phosphorylation / arginine dephosphorylation / phosphatase reaction intermediate / LMW PTP / phosphorylation at Ser6 | ||||||
Function / homology | Function and homology information protein arginine phosphatase / protein arginine phosphatase activity / protein tyrosine phosphatase activity Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fuhrmann, J. / Clausen, T. | ||||||
Citation | Journal: Cell Rep / Year: 2013 Title: Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria. Authors: Fuhrmann, J. / Mierzwa, B. / Trentini, D.B. / Spiess, S. / Lehner, A. / Charpentier, E. / Clausen, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kk4.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kk4.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 4kk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kk4_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 4kk4_full_validation.pdf.gz | 423.5 KB | Display | |
Data in XML | 4kk4_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4kk4_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/4kk4 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/4kk4 | HTTPS FTP |
-Related 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: 17116.391 Da / Num. of mol.: 1 / Mutation: C7S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: ywlE, BSU36930, ipc-31d / Production host: Escherichia coli (E. coli) / References: UniProt: P39155, protein-tyrosine-phosphatase |
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#2: 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: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 30% PEG400, 50 mM Tris-HCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→42.919 Å / Num. all: 12470 / Num. obs: 12470 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.053 / Net I/σ(I): 11.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→18.414 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8579 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 21.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.5 Å2 / Biso mean: 36.7686 Å2 / Biso min: 14.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→18.414 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: 12.7906 Å / Origin y: -18.2339 Å / Origin z: 12.347 Å
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Refinement TLS group | Selection details: all |