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- PDB-4ne2: Pantothenamide-bound Pantothenate Kinase from Klebsiella pneumoniae -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ne2 | ||||||
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Title | Pantothenamide-bound Pantothenate Kinase from Klebsiella pneumoniae | ||||||
![]() | Pantothenate kinase | ||||||
![]() | TRANSFERASE / Protein-substrate complex | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Hughes, S.J. / Antoshchenko, T. / Kim, K.P. / Smil, D. / Park, H.W. | ||||||
![]() | ![]() Title: Structural characterization of a new N-substituted pantothenamide bound to pantothenate kinases from Klebsiella pneumoniae and Staphylococcus aureus. Authors: Hughes, S.J. / Antoshchenko, T. / Kim, K.P. / Smil, D. / Park, H.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 290.3 KB | Display | ![]() |
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PDB format | ![]() | 233.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nb4C ![]() 4gi7S 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 38460.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.67 % |
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Crystal grow | Temperature: 289 K / pH: 8.5 Details: 0.5 uL protein + 0.5 uL buffer (2M sodium formate, 0.1M Tris HCl), pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 28, 2013 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 68657 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.453 / % possible all: 100 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 4GI7 Resolution: 1.9→39.63 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.748 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN
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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 mean: 34.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.63 Å
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Refine LS restraints |
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