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Open data
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Basic information
Entry | Database: PDB / ID: 4uxw | ||||||
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Title | Structure of delta4-DgkA-apo in 9.9 MAG | ||||||
![]() | DIACYLGLYCEROL KINASE![]() | ||||||
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Function / homology | ![]() diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, D. / Pye, V.E. / Aragao, D. / Caffrey, M. | ||||||
![]() | ![]() Title: Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase. Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / ...Authors: Li, D. / Stansfeld, P.J. / Sansom, M.S.P. / Keogh, A. / Vogeley, L. / Howe, N. / Lyons, J.A. / Aragao, D. / Fromme, P. / Fromme, R. / Basu, S. / Grotjohann, I. / Kupitz, C. / Rendek, K. / Weierstall, U. / Zatsepin, N.A. / Cherezov, V. / Liu, W. / Bandaru, S. / English, N.J. / Gati, C. / Barty, A. / Yefanov, O. / Chapman, H.N. / Diederichs, K. / Messerschmidt, M. / Boutet, S. / Williams, G.J. / Marvin Seibert, M. / Caffrey, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.2 KB | Display | ![]() |
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PDB format | ![]() | 120.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4uxxC ![]() 4uxzC ![]() 4uyoC ![]() 3ze5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 14240.527 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-OLC / ( #3: Chemical | ChemComp-MPD / ( | ![]() #4: Chemical | ChemComp-NO3 / | ![]() #5: Chemical | ChemComp-NA / | Sequence details | THE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN ...THE PROTEIN CONTAINS AN N-TERMINAL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS FOUR MUTATIONS. THEY ARE I53V, I70L, M96L AND V107D. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.14 % / Description: NONE |
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Crystal grow![]() | Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6 Details: 7-10 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 7-10 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM NITRATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 9.9 MONOACYLGLYCEROL (9.9 MAG) AS THE HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 21, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.15→45.73 Å / Num. obs: 11151 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 109.78 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.15→3.23 Å / Redundancy: 11 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.4 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3ZE5 Resolution: 3.15→45.733 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 29.49 / Stereochemistry target values: ML Details: THERE ARE THREE NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS RESTRAINTS WERE NOT USED IN THE REFINEMENT.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.8 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→45.733 Å
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Refine LS restraints |
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LS refinement shell |
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