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Open data
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Basic information
Entry | Database: PDB / ID: 4mb2 | ||||||
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Title | Crystal structure of TON1374 in complex with ATP | ||||||
![]() | Phosphopantothenate synthetase | ||||||
![]() | LIGASE / ATP binding | ||||||
Function / homology | ![]() 4-phosphopantoate-beta-alanine ligase / acid-amino acid ligase activity / coenzyme A biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, M.-K. / An, Y.J. / Cha, S.-S. | ||||||
![]() | ![]() Title: The crystal structure of a novel phosphopantothenate synthetase from the hyperthermophilic archaea, Thermococcus onnurineus NA1 Authors: Kim, M.-K. / An, Y.J. / Cha, S.-S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 211.1 KB | Display | ![]() |
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PDB format | ![]() | 171.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 56.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 29732.498 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 8.5 Details: 0.08M Tris-HCl, 24%(w/v) polyethylene glycol 4000, 4mM ATP, pH 8.5, VAPOR DIFFUSION, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 26, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. all: 60918 / Num. obs: 60918 / % possible obs: 97.8 % / Observed criterion σ(I): 4.8 |
Reflection shell | Resolution: 2.19→2.23 Å / % possible all: 92.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 171.19 Å2 / Biso mean: 48.6026 Å2 / Biso min: 11.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→37.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.192→2.249 Å / Total num. of bins used: 20
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