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Yorodumi- PDB-4nb4: Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nb4 | ||||||
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Title | Pantothenamide-bound Pantothenate kinase from Staphylococcus aureus | ||||||
Components | Type II pantothenate kinase | ||||||
Keywords | TRANSFERASE / Protein-Substrate 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | ||||||
Authors | Hughes, S.J. / Antoshchenko, T. / Smil, D. / Park, H.W. | ||||||
Citation | Journal: Proteins / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nb4.cif.gz | 424 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nb4.ent.gz | 347.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nb4 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nb4 | HTTPS FTP |
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-Related structure data
Related structure data | 4ne2C 2ewsS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 2 / Auth seq-ID: 16 - 23 / Label seq-ID: 34 - 41
NCS ensembles :
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-Components
#1: Protein | Mass: 31327.312 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: CoaA, coaW / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6G7I0, pantothenate kinase #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-SH3 / #4: Chemical | ChemComp-MG / #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: 2.09 Å3/Da / Density % sol: 41.01 % |
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Crystal grow | Temperature: 289 K / pH: 7.5 Details: 0.5 uL protein + 0.5 uL buffer (1.4 M sodium citrate, 0.1 M HEPES, 5% ethylene glycol), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 |
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: 2.25→40 Å / Num. obs: 97518 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.094 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.301 / % possible all: 99.2 |
-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 2EWS Resolution: 2.25→39.91 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.832 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.804 / SU ML: 0.223 / SU R Cruickshank DPI: 0.4497 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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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: 22.64 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.91 Å
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Refine LS restraints |
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