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Yorodumi- PDB-5mqh: Structure of the Phosphatase Domain of the Cell Fate Determinant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mqh | ||||||
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Title | Structure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis in a crystal form without domain swapping | ||||||
Components | Serine phosphatase | ||||||
Keywords | TRANSFERASE / Sporulation / Phosphatase / PP2C / Manganese | ||||||
Function / homology | Function and homology information endospore-forming forespore / myosin phosphatase activity / sporulation resulting in formation of a cellular spore / protein-serine/threonine phosphatase / phosphatase activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Levdikov, V.M. / Wilkinson, A.J. / Blagova, E.V. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2017 Title: A widespread family of serine/threonine protein phosphatases shares a common regulatory switch with proteasomal proteases. Authors: Bradshaw, N. / Levdikov, V.M. / Zimanyi, C.M. / Gaudet, R. / Wilkinson, A.J. / Losick, R. #1: Journal: J. Mol. Biol. / Year: 2012 Title: Structure of the phosphatase domain of the cell fate determinant SpoIIE from Bacillus subtilis. Authors: Levdikov, V.M. / Blagova, E.V. / Rawlings, A.E. / Jameson, K. / Tunaley, J. / Hart, D.J. / Barak, I. / Wilkinson, A.J. #2: Journal: Elife / Year: 2015 Title: Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase. Authors: Bradshaw, N. / Losick, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mqh.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqh.ent.gz | 42.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mqh_validation.pdf.gz | 431.5 KB | Display | wwPDB validaton report |
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Full document | 5mqh_full_validation.pdf.gz | 434.3 KB | Display | |
Data in XML | 5mqh_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 5mqh_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqh ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqh | HTTPS FTP |
-Related structure data
Related structure data | 5ucgC 3t9lS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 27417.348 Da / Num. of mol.: 1 / Mutation: A624I Source method: isolated from a genetically manipulated source Details: The mutation Ala624 to Ile was introduced to reduce successfully the extent of domain swapping. Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SC09_Contig28orf00413 / Plasmid: pETYSBLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D1KMY9, UniProt: P37475*PLUS |
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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: 2.57 Å3/Da / Density % sol: 52.13 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2M Sodium formate, 0.1M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→61.34 Å / Num. obs: 10961 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rsym value: 0.057 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.44→2.48 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.8 / CC1/2: 0.874 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3T9L Resolution: 2.45→48.99 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.871 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.958 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→48.99 Å
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Refine LS restraints |
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