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- PDB-3bex: Type III pantothenate kinase from Thermotoga maritima complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bex | ||||||
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Title | Type III pantothenate kinase from Thermotoga maritima complexed with pantothenate | ||||||
![]() | Type III pantothenate kinase | ||||||
![]() | TRANSFERASE / Actin-like fold / ATP-binding / Coenzyme A biosynthesis / Cytoplasm / Kinase / Metal-binding / Nucleotide-binding / Potassium | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yang, K. / Huerta, C. / Strauss, E. / Zhang, H. | ||||||
![]() | ![]() Title: Structural basis for substrate binding and the catalytic mechanism of type III pantothenate kinase. Authors: Yang, K. / Strauss, E. / Huerta, C. / Zhang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 332.3 KB | Display | ![]() |
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PDB format | ![]() | 268.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.6 KB | Display | ![]() |
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Full document | ![]() | 528.2 KB | Display | |
Data in XML | ![]() | 75.6 KB | Display | |
Data in CIF | ![]() | 109.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bf1C ![]() 3bf3C ![]() 2gtdS 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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Unit cell |
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Components
#1: Protein | Mass: 27530.719 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-PAU / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 16% PEG 2250, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.51→50 Å / Num. obs: 209057 / % possible obs: 99.7 % / Rsym value: 0.061 / Net I/σ(I): 11.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2GTD Resolution: 1.51→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.37 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084 / 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: 21.423 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.551 Å / Total num. of bins used: 20
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