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- PDB-6ebv: Staphylococcus aureus Type II pantothenate kinase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ebv | ||||||
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Title | Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-N7-Pan | ||||||
![]() | Type II pantothenate kinase | ||||||
![]() | TRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog | ||||||
Function / homology | ![]() pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H. / Park, H. | ||||||
![]() | ![]() Title: Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase. Authors: Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.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 | ![]() | 215.1 KB | Display | ![]() |
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PDB format | ![]() | 172.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 39.3 KB | Display | |
Data in CIF | ![]() | 51.9 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: 29126.949 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: coaW, BTN44_13005, C3B39_13135, EP54_10775, EQ90_06670, HMPREF3211_02599 Production host: ![]() ![]() References: UniProt: A0A0D6HHM8, UniProt: Q2FWC7*PLUS, pantothenate kinase #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-27Q / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, 33% PEG4000, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 16, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.62 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 21357 / % possible obs: 97.5 % / Redundancy: 2.81 % / Net I/σ(I): 5.82 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 2.79 % / Mean I/σ(I) obs: 2.14 / Num. unique obs: 3421 / % possible all: 97.7 |
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Processing
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Refinement | Resolution: 3→44.49 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.76 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.512
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Displacement parameters | Biso max: 128.36 Å2 / Biso mean: 42.7 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.47 Å | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→44.49 Å
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LS refinement shell | Resolution: 3→3.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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