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Yorodumi- PDB-4m7y: Staphylococcus aureus Type II pantothenate kinase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m7y | ||||||
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Title | Staphylococcus aureus Type II pantothenate kinase in complex with a pantothenate analog | ||||||
Components | Type II pantothenate kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / pantothenate kinase / inhibitor / antibacterial / Structural Genomics / Structural Genomics Consortium / SGC / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Mottaghi, K. / Hong, B. / Tempel, W. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: ACS Infect Dis / Year: 2016 Title: Discovery of Potent Pantothenamide Inhibitors of Staphylococcus aureus Pantothenate Kinase through a Minimal SAR Study: Inhibition Is Due to Trapping of the Product. Authors: Hughes, S.J. / Barnard, L. / Mottaghi, K. / Tempel, W. / Antoshchenko, T. / Hong, B.S. / Allali-Hassani, A. / Smil, D. / Vedadi, M. / Strauss, E. / Park, H.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m7y.cif.gz | 227.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m7y.ent.gz | 180.8 KB | Display | PDB format |
PDBx/mmJSON format | 4m7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/4m7y ftp://data.pdbj.org/pub/pdb/validation_reports/m7/4m7y | HTTPS FTP |
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-Related structure data
Related structure data | 4m7xSC 5elzC 5jicC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29955.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: MW2 / Gene: coaW, MW2054 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-TR / References: UniProt: Q8NVG0, pantothenate kinase |
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-Non-polymers , 5 types, 226 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-UNX / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.3 % |
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Crystal grow | Method: vapor diffusion / pH: 7 Details: 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. Crystal condition: 2.5 M ammonium sulfate, 0.1 M BTP, 1.1 % w/v Cyclohexylethanoyl-N- ...Details: 0.01 M inhibitor, 0.01 M magnesium chloride, 0.01 M ATP were added to the protein sample. Crystal condition: 2.5 M ammonium sulfate, 0.1 M BTP, 1.1 % w/v Cyclohexylethanoyl-N-hydroxyethylglucamide., pH 7.0, vapor diffusion |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 24, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→30 Å / Num. obs: 48878 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.94 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.87 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4m7x Resolution: 1.8→26.532 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.167 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 6.661 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. INHIBITOR RESTRAINTS WERE BASED ON PRODRG CALCULATIONS. COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. INHIBITOR RESTRAINTS WERE BASED ON PRODRG CALCULATIONS. COOT AND THE MOLPROBITY SERVER WERE ALSO USED DURING REFINEMENT. SOME DUMMY ATOMS AND PHOSPHATE IONS B303, B304, A303, B305 OF THE MODEL REPRESENT ELECTRON DENSITY THAT APPEARS TO ARISE FROM A LARGER, UNIDENTIFIED MOLECULE.
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.01 Å2 / Biso mean: 31.734 Å2 / Biso min: 15.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→26.532 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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