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Yorodumi- PDB-6awj: Staphylococcus aureus Type II pantothenate kinase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6awj | ||||||
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Title | Staphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-MeO-N5Pan with pantothenate present in reaction | ||||||
Components | Type II pantothenate kinase | ||||||
Keywords | TRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog | ||||||
Function / homology | Function and homology information pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H. | ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6awj.cif.gz | 216.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6awj.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 6awj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6awj_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6awj_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6awj_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 6awj_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/6awj ftp://data.pdbj.org/pub/pdb/validation_reports/aw/6awj | HTTPS FTP |
-Related structure data
-Links
-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: 28997.770 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: coaW, AYM28_11860, AYM37_11860, ERS072738_01917, ERS074020_01878, HMPREF3211_02599 Production host: Escherichia coli (E. coli) References: UniProt: A0A0D6HHM8, UniProt: Q2FWC7*PLUS, pantothenate kinase #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-N7G / ( #4: 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: 2.38 Å3/Da / Density % sol: 48.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2016 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→132 Å / Num. obs: 38162 / % possible obs: 99.7 % / Redundancy: 3.54 % / Net I/σ(I): 7.75 |
Reflection shell | Highest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.884 / SU B: 13.972 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.111 / ESU R Free: 0.327 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.22 Å2 / Biso mean: 35.878 Å2 / Biso min: 2.75 Å2
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Refinement step | Cycle: final / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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