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Yorodumi- PDB-6awg: Staphylococcus aureus Type II pantothenate kinase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6awg | ||||||
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Title | Staphylococcus aureus Type II pantothenate kinase in complex with nucleotides and pantothenate analog Deoxy-N190Pan | ||||||
Components | Type II pantothenate kinase | ||||||
Keywords | TRANSFERASE / Staphylococcus aureus / SaPanK / ADP / ATP / 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: 2.4 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 | 6awg.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6awg.ent.gz | 177.6 KB | Display | PDB format |
PDBx/mmJSON format | 6awg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6awg_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6awg_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6awg_validation.xml.gz | 41.3 KB | Display | |
Data in CIF | 6awg_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/6awg ftp://data.pdbj.org/pub/pdb/validation_reports/aw/6awg | 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 | #3: Chemical | ChemComp-C0G / ( #4: Chemical | #5: 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: 2.4 Å3/Da / Density % sol: 48.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5 |
-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: DECTRIS PILATUS3 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: 1.8→132.4 Å / Num. obs: 43566 / % possible obs: 99.5 % / Redundancy: 3.91 % / Net I/σ(I): 10.41 |
Reflection shell | Highest resolution: 1.8 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.797 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.534 / ESU R Free: 0.298 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: 99.67 Å2 / Biso mean: 33.395 Å2 / Biso min: 7.71 Å2
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Refinement step | Cycle: final / Resolution: 2.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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