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Yorodumi- PDB-2e1y: Crystal structure of propionate kinase (TdcD) from Salmonella typ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e1y | ||||||
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Title | Crystal structure of propionate kinase (TdcD) from Salmonella typhimurium | ||||||
Components | Propionate kinase | ||||||
Keywords | TRANSFERASE / Propionate kinase / TdcD / Native / Acetate kinase / Nucleotide / Ap4A / ADP / ATP / AMPPNP | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity. Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.N. #1: Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R. #2: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2005 Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of propionate kinase (TdcD) from Salmonella typhimurium Authors: Simanshu, D.K. / Murthy, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e1y.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e1y.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2e1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/2e1y ftp://data.pdbj.org/pub/pdb/validation_reports/e1/2e1y | HTTPS FTP |
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-Related structure data
Related structure data | 2e1zC 2e20C 1x3mS 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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-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: IFO 12529 / Gene: tdcD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21pLysS / References: UniProt: O06961, propionate kinase |
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#2: 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: 2.61 Å3/Da / Density % sol: 52.79 % |
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Crystal grow | Temperature: 293 K / Method: microbatch method / pH: 6.5 Details: 0.1 Bis-Tris pH 6.5, 30% (v/v) pentaerythritol ethoxylate (15/4 EO/OH), Microbatch method, temperature 293K |
-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: Nov 29, 2005 / Details: Osmic mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 14818 / % possible obs: 98.3 % / Redundancy: 33.56 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1235 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1X3M Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 12.101 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.847 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 34.052 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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