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Yorodumi- PDB-4fwo: Crystal structure of Salmonella typhimurium propionate kinase (Td... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fwo | ||||||
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Title | Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GMP | ||||||
Components | Propionate kinase | ||||||
Keywords | TRANSFERASE / Kinase / Acetate and Sugar Kinases/Hsc70/Actin (ASKHA) superfamily / Propionate kinase / TdcD / GMP / Short-Chain Fatty Acid | ||||||
Function / homology | Function and homology information propionate kinase / propionate kinase activity / L-threonine catabolic process to propionate / acetate kinase activity / acetate metabolic process / phosphorylation / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | ||||||
Authors | Chittori, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies. Authors: Chittori, S. / Simanshu, D.K. / Banerjee, S. / Murthy, A.M.V. / Mathivanan, S. / Savithri, H.S. / Murthy, M.R.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fwo.cif.gz | 90.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwo.ent.gz | 66.1 KB | Display | PDB format |
PDBx/mmJSON format | 4fwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwo ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwo | HTTPS FTP |
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-Related structure data
Related structure data | 4fwkC 4fwlC 4fwmC 4fwnC 4fwpC 4fwqC 4fwrC 4fwsC 2e1yS 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
#1: Protein | Mass: 45246.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: oxd-2, STM3242, tdcD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06961, propionate kinase | ||||
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#2: Chemical | #3: Chemical | ChemComp-5GP / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.08 % / Mosaicity: 2.506 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris pH 6.0, 35% Pentaerythritol ethoxylate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 4, 2008 / Details: Mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→50 Å / Num. obs: 10515 / % possible obs: 97.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.142 / Χ2: 1.006 / Net I/σ(I): 62.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 2E1Y Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.857 / Occupancy max: 1 / Occupancy min: 1 / SU B: 18.77 / SU ML: 0.366 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 85.93 Å2 / Biso mean: 44.3506 Å2 / Biso min: 3.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.901→2.976 Å / Total num. of bins used: 20
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