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- PDB-3w40: Crystal structure of RsbX in complex with magnesium in space group P1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w40 | ||||||
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Title | Crystal structure of RsbX in complex with magnesium in space group P1 | ||||||
![]() | Phosphoserine phosphatase RsbX | ||||||
![]() | 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 | ![]() phosphoserine phosphatase / L-phosphoserine phosphatase activity / phosphoprotein phosphatase activity / response to heat Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Teh, A.H. / Makino, M. / Baba, S. / Shimizu, N. / Yamamoto, M. / Kumasaka, T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.5 KB | Display | ![]() |
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PDB format | ![]() | 163.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 37.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3w41C ![]() 3w42C ![]() 3w43C ![]() 3w44C ![]() 3w45SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % |
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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, pH 8.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 1, 2006 |
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: 1.3→50 Å / Num. obs: 75857 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rsym value: 0.076 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2.2 % / Rsym value: 0.325 / % possible all: 68.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3W45 Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2217 / WRfactor Rwork: 0.1719 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8467 / SU B: 2.289 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0806 / SU Rfree: 0.0739 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.074 / 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: 78.41 Å2 / Biso mean: 15.0362 Å2 / Biso min: 2.96 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
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