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Yorodumi- PDB-1x3m: Crystal structure of ADP bound Propionate kinase (TdcD) from Salm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x3m | ||||||
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Title | Crystal structure of ADP bound Propionate kinase (TdcD) from Salmonella typhimurium | ||||||
Components | Propionate kinase | ||||||
Keywords | TRANSFERASE / Propionate Kinase / TdcD / ADP / L-threonine metabolism / Propionate Metabolism | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Simanshu, D.K. / Savithri, H.S. / Murthy, M.R. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x3m.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x3m.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 1x3m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/1x3m ftp://data.pdbj.org/pub/pdb/validation_reports/x3/1x3m | HTTPS FTP |
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-Related structure data
Related structure data | 1x3nC 1g99S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The second part of the biological assembly is generated by the two fold axis:Y, X, -Z |
-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) / Gene: tdcD / Plasmid: pRSET-c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O06961, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a carboxy group as acceptor |
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#2: Chemical | ChemComp-ADP / |
#3: 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: 2.7 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: PEGMME500, PEGMME2000, PEGMME5000, Bis-Tris, Pentaerythritol ethoxylate, pH 6.5, VAPOR DIFFUSION, temperature 291K |
-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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 2004 / Details: Osmic 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: 2.2→35 Å / Num. obs: 22939 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.58 % / Biso Wilson estimate: 38.39 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.55 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.88 / Num. unique all: 424150 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Acetate kinase (PDB:1G99) Resolution: 2.2→31.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 393025.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: Coordinates of the residues ranging from 39 to 42 and 49 to 58 are tentatie due to poor electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.985 Å2 / ksol: 0.350611 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→31.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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