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Yorodumi- PDB-4up6: Crystal structure of the wild-type diacylglycerol kinase refolded... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4up6 | ||||||
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Title | Crystal structure of the wild-type diacylglycerol kinase refolded in the lipid cubic phase | ||||||
Components | DIACYLGLYCEROL KINASE | ||||||
Keywords | TRANSFERASE / 7.8 MAG / IN MESO / IN VITRO FOLDING / LIPID CUBIC PHASE / MEMBRANE PROTEIN / MONOACYLGLYCEROL / REFOLDING / RENATURATION | ||||||
Function / homology | Function and homology information diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / phosphorylation / ATP binding / membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.801 Å | ||||||
Authors | Li, D. / Caffrey, M. | ||||||
Citation | Journal: Sci.Rep. / Year: 2014 Title: Renaturing Membrane Proteins in the Lipid Cubic Phase, a Nanoporous Membrane Mimetic. Authors: Li, D. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4up6.cif.gz | 70.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4up6.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 4up6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4up6 ftp://data.pdbj.org/pub/pdb/validation_reports/up/4up6 | HTTPS FTP |
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-Related structure data
Related structure data | 4brbC 3ze4S 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: 14252.625 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PTRCHISB-DGKA-WT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP) Sequence details | AN N-TERMINAL TAG (GHHHHHHEL) WAS ADDED TO AID PROTEIN PURIFICATION. THE N-TERMINAL MET IS CLEAVED, ...AN N-TERMINAL TAG (GHHHHHHEL) WAS ADDED TO AID PROTEIN PURIFICATI | |
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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: 3.99 Å3/Da / Density % sol: 69.23 % / Description: NONE |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase / pH: 5.6 Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 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 DEGREE ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 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 DEGREE CELSIUS WITH THE 7.8 MONOACYLGLYCEROL (7.8 MAG) AS THE HOSTING LIPID. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 16, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→54.44 Å / Num. obs: 6532 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 136.72 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 3.8→3.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZE4 Resolution: 3.801→46.323 Å / SU ML: 0.59 / σ(F): 1.34 / Phase error: 43.17 / Stereochemistry target values: ML Details: THERE ARE THREE IDENTICAL MONOMERS IN THE ASYMMETRIC UNIT. NCS RESTRAINTS WERE APPLIED FOR TORSION ANGLES DURING 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: 145.86 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.801→46.323 Å
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Refine LS restraints |
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LS refinement shell |
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