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- PDB-3s40: The crystal structure of a diacylglycerol kinases from Bacillus a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3s40 | ||||||
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Title | The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne | ||||||
![]() | diacylglycerol kinase![]() | ||||||
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Function / homology | ![]() phospholipid biosynthetic process / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Zhang, R. / Xu, X. / Cui, H. / Peterson, S. / Savchenko, A. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: The crystal structure of a diacylglycerol kinases from Bacillus anthracis str. Sterne Authors: Tan, K. / Zhang, R. / Xu, X. / Cui, H. / Peterson, S. / Savchenko, A. / Anderson, W.F. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 444.3 KB | Display | ![]() |
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PDB format | ![]() | 365.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2qvlS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Experimentally unknown. It is predicted that the molecule is monomeric. |
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Components
#1: Protein | ![]() Mass: 33369.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.14 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: 0.1M Bis-Tris, 0.4M NH4Cl, 16% PEG 3350, 4% Jeffamine M-600, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2010 / Details: Mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→44 Å / Num. all: 62575 / Num. obs: 62575 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 1.4 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2QVL Resolution: 2.1→43.231 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 24.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.943 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→43.231 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 25.7048 Å / Origin y: 33.0817 Å / Origin z: 37.1669 Å
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Refinement TLS group | Selection details: all |