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Yorodumi- PDB-2p1r: Crystal structure of Salmonella typhimurium YegS, a putative lipi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2p1r | ||||||
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Title | Crystal structure of Salmonella typhimurium YegS, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases. | ||||||
Components | Lipid kinase yegS | ||||||
Keywords | TRANSFERASE / YegS / diacylglycerol / kinase / lipid / ATP-binding / Magnesium / Metal-binding / ---- | ||||||
Function / homology | Function and homology information lipid kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / NAD+ kinase activity / phospholipid biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Nichols, C.E. / Lamb, H.K. / Lockyer, M. / Charles, I.G. / Pyne, S. / Hawkins, A.R. / Stammers, D.K. | ||||||
Citation | Journal: Proteins: Struct.,Funct.,Genet. / Year: 2007 Title: Characterization of Salmonella typhimurium YegS, a putative lipid kinase homologous to eukaryotic sphingosine and diacylglycerol kinases Authors: Nichols, C.E. / Lamb, H.K. / Lockyer, M. / Charles, I.G. / Pyne, S. / Hawkins, A.R. / Stammers, D.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p1r.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p1r.ent.gz | 193.8 KB | Display | PDB format |
PDBx/mmJSON format | 2p1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/2p1r ftp://data.pdbj.org/pub/pdb/validation_reports/p1/2p1r | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Chains A and C form one biological dimer, Chains B and D form a second dimer. |
-Components
#1: Protein | Mass: 32385.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: yegS / Plasmid: pRF69 / Production host: Escherichia coli (E. coli) / Strain (production host): B384pLysS References: UniProt: Q8ZNP1, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor #2: Chemical | #3: Chemical | ChemComp-CA / #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: 2.63 Å3/Da / Density % sol: 53.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: pH 7.4, 17% PEG3350, 0.2M ammonium sulphate. VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.885596, 0.979239, 0.885596 | |||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 4, 2004 Details: Si(111) monochromator. Mirror 1: Grazing angle 2.8 mrad, vertical focusing. Mirror 2: vertical and horizontal focusing. | |||||||||
Radiation | Monochromator: Si(111) monochromator. / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.5→30 Å / Num. all: 46970 / Num. obs: 45865 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6.2 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.46 | |||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.74 / Num. unique all: 3506 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1492706.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -1.8 / ESU R: 0.746 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.4313 Å2 / ksol: 0.303722 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 42.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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