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Yorodumi- PDB-2j6z: Structural and functional characterisation of partner-switching r... -
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-Basic information
Entry | Database: PDB / ID: 2j6z | ||||||
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Title | Structural and functional characterisation of partner-switching regulating the environmental stress response in B. subtilis | ||||||
Components | PHOSPHOSERINE PHOSPHATASE RSBU | ||||||
Keywords | HYDROLASE / PARTNER SWITCHING / PROTEIN PHOSPHATASE / RSBT / RSBU / BACILLUS SUBTILIS / ENVIRONMENTAL STRESS | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Hardwick, S.W. / Pane-Farre, J. / Delumeau, O. / Marles-Wright, J. / Murray, J.W. / Hecker, M. / Lewis, R.J. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2007 Title: Structural and functional characterization of partner switching regulating the environmental stress response in Bacillus subtilis. Authors: Hardwick, S.W. / Pane-Farre, J. / Delumeau, O. / Marles-Wright, J. / Murray, J.W. / Hecker, M. / Lewis, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j6z.cif.gz | 30.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j6z.ent.gz | 20.2 KB | Display | PDB format |
PDBx/mmJSON format | 2j6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j6z_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 2j6z_full_validation.pdf.gz | 422.7 KB | Display | |
Data in XML | 2j6z_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 2j6z_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/2j6z ftp://data.pdbj.org/pub/pdb/validation_reports/j6/2j6z | HTTPS FTP |
-Related structure data
Related structure data | 2j6yC 2j70C 1w53S 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
#1: Protein | Mass: 13127.001 Da / Num. of mol.: 1 / Fragment: RSBT BINDING DOMAIN, RESIDUES 1-111 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): DE3 / References: UniProt: P40399, phosphoserine phosphatase | ||
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#2: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | RESIDUE Y28 HAS BEEN MUTATED TO I | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.51 Å3/Da / Density % sol: 18.56 % |
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Crystal grow | pH: 6.5 / Details: 10 % PEG 20000, 100 MM MES PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 28, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→28.8 Å / Num. obs: 5862 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1W53 Resolution: 1.95→24.23 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.856 / SU B: 5.696 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→24.23 Å
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Refine LS restraints |
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