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Yorodumi- PDB-3w42: Crystal structure of RsbX in complex with manganese in space group P1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w42 | ||||||
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Title | Crystal structure of RsbX in complex with manganese in space group P1 | ||||||
Components | Phosphoserine phosphatase RsbX | ||||||
Keywords | HYDROLASE / Signaling protein / Stressosome / Environmental stress / Phosphoric Monoester Hydrolases / Dephosphorylation / Tertiary / phosphatase / Protein phosphatase / magnesium/manganese binding / alpha-beta beta-alpha sandwich fold | ||||||
Function / homology | Function and homology information phosphoserine phosphatase / L-phosphoserine phosphatase activity / phosphoprotein phosphatase activity / response to heat Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | ||||||
Authors | Teh, A.H. / Makino, M. / Baba, S. / Shimizu, N. / Yamamoto, M. / Kumasaka, T. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Structure of the RsbX phosphatase involved in the general stress response of Bacillus subtilis Authors: Teh, A.H. / Makino, M. / Hoshino, T. / Baba, S. / Shimizu, N. / Yamamoto, M. / Kumasaka, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w42.cif.gz | 206.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w42.ent.gz | 165.4 KB | Display | PDB format |
PDBx/mmJSON format | 3w42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/3w42 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/3w42 | HTTPS FTP |
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-Related structure data
Related structure data | 3w40C 3w41C 3w43C 3w44C 3w45SC 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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-Components
#1: Protein | Mass: 22172.029 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU04740, rsbX / Plasmid: pTYB11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17906, phosphoserine phosphatase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-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: 298 K / Method: vapor diffusion / pH: 8.5 Details: 20 % PEG 1000, 0.1M Tris-HCl, 5mM MgCl2, 3mM MnCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: KIRKPATRICK-BAEZ MIRRORS |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.06→50 Å / Num. obs: 155995 / % possible obs: 90.3 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.081 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.06→1.1 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.366 / % possible all: 71.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3W45 Resolution: 1.06→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.02 / SU B: 0.756 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0284 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.03 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.484 Å2
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Refinement step | Cycle: LAST / Resolution: 1.06→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.061→1.088 Å / Total num. of bins used: 20
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