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Yorodumi- PDB-3w43: Crystal structure of RsbX in complex with manganese in space group P21 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w43 | ||||||
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Title | Crystal structure of RsbX in complex with manganese in space group P21 | ||||||
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: 1.22 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 | 3w43.cif.gz | 109.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w43.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 3w43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3w43_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
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Full document | 3w43_full_validation.pdf.gz | 422.8 KB | Display | |
Data in XML | 3w43_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3w43_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/3w43 ftp://data.pdbj.org/pub/pdb/validation_reports/w4/3w43 | HTTPS FTP |
-Related structure data
Related structure data | 3w40C 3w41C 3w42C 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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Unit cell |
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-Components
#1: Protein | Mass: 22172.029 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | #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: 2.01 Å3/Da / Density % sol: 38.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 8.5 Details: 10% PEG 1000, 0.1M Tris-HCl, 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: BL38B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 7, 2009 / Details: Toroidal Mirror |
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: 1.22→50 Å / Num. obs: 50676 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.035 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.22→1.26 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.396 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3W45 Resolution: 1.22→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1944 / WRfactor Rwork: 0.1559 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8947 / SU B: 1.369 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0501 / SU Rfree: 0.048 / Cross valid method: THROUGHOUT / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.36 Å2 / Biso mean: 15.5347 Å2 / Biso min: 5.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.22→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.251 Å / Total num. of bins used: 20
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