+Open data
-Basic information
Entry | Database: PDB / ID: 2jgr | ||||||
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Title | Crystal structure of YegS in complex with ADP | ||||||
Components | YEGS | ||||||
Keywords | TRANSFERASE / PHOSPHATIDYLGLYCEROLE KINASE / LIPID KINASE / PYRROPHOSPHATE / HYPOTHETICAL PROTEIN | ||||||
Function / homology | Function and homology information lipid kinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / phospholipid biosynthetic process / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Bakali, H.M. / Herman, M.D. / Johnson, K.A. / Kelly, A.A. / Wieslander, A. / Hallberg, B.M. / Nordlund, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure of Yegs, a Homologue to the Mammalian Diacylglycerol Kinases, Reveals a Novel Regulatory Metal Binding Site. Authors: Bakali, H.M. / Herman, M.D. / Johnson, K.A. / Kelly, A.A. / Wieslander, A. / Hallberg, B.M. / Nordlund, P. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jgr.cif.gz | 64.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgr.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgr ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgr | HTTPS FTP |
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-Related structure data
Related structure data | 2bonSC 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: 32394.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21List of strains of Escherichia coli / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P76407 |
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#2: Chemical | ChemComp-POP / |
#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: 3.26 Å3/Da / Density % sol: 62.31 % |
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→88 Å / Num. obs: 11841 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BON Resolution: 2.65→88.39 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 22.407 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.402 / ESU R Free: 0.28 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→88.39 Å
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Refine LS restraints |
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