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- PDB-5d57: In meso X-ray crystallography structure of diacylglycerol kinase,... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5d57 | ||||||
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Title | In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K | ||||||
![]() | Diacylglycerol kinase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, C.-Y. / Howe, N. / Olieric, V. / Wang, M. / Caffrey, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, 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 | ![]() | 132.3 KB | Display | ![]() |
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PDB format | ![]() | 106 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 34.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5d52C ![]() 5d53C ![]() 5d54C ![]() 5d56C ![]() 5d58C ![]() 5d59C ![]() 5d5aC ![]() 5d5bC ![]() 5d5cC ![]() 5d5dC ![]() 5d5eC ![]() 5d5fC ![]() 3ze3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: A41C, C46A, I53V, I70L, M96L, V107D and C113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-78M / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.49 % |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase Details: 3-6 %(v/v) MPD, 0.1 M NaCl, 60 mM Mg(CH3COO)2 and 50 mM Na3C6H5O7, pH 5.6 PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 24904 / % possible obs: 99.6 % / Redundancy: 6.23 % / Net I/σ(I): 7.71 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 5.63 % / Mean I/σ(I) obs: 1.61 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ze3 Resolution: 2.8→45.67 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.67 Å
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Refine LS restraints |
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LS refinement shell |
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