+Open data
-Basic information
Entry | Database: PDB / ID: 4uxx | |||||||||
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Title | Structure of delta4-DgkA with AMPPCP in 9.9 MAG | |||||||||
Components | DIACYLGLYCEROL KINASE | |||||||||
Keywords | TRANSFERASE / ATP ANALOGUE / DGKA / DIACYLGLYEROL KINASE / IN MESO CRYSTALLIZATION / LIPID CUBIC PHASE / LIPIDIC CUBIC PHASE / LIPID MESOPHASE / LIPIDIC MESOPHASE / MEMBRANE PROTEIN / 9.9 MAG / MONOACYLGLYCEROL / NON- HYDROLYZABLE ATP ANALOGUE / NUCLEOTIDE ANALOGUE | |||||||||
Function / homology | Function and homology information diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ESCHERICHIA COLI K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å | |||||||||
Authors | Li, D. / Vogeley, L. / Caffrey, M. | |||||||||
Citation | Journal: Nat.Commun. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uxx.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uxx.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 4uxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4uxx_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4uxx_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4uxx_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4uxx_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/4uxx ftp://data.pdbj.org/pub/pdb/validation_reports/ux/4uxx | HTTPS FTP |
-Related structure data
Related structure data | 4uxwC 4uxzC 4uyoC 3ze5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 14240.527 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PTRCHISB-DGKA-DELTA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP) |
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-Non-polymers , 8 types, 30 molecules
#2: Chemical | ChemComp-CL / | ||||||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-OLC / ( #6: Chemical | ChemComp-MPD / ( | #7: Chemical | #8: Chemical | ChemComp-ACP / | #9: Water | ChemComp-HOH / | |
-Details
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: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.85 % Description: FOUR CRYSTALS WERE USED FOR THE NATIVE DATA SET. A SINGLE CRYSTAL WAS USED FOR THE ZN-ANOMALOUS DATA SET. |
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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 (LIPID 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 (LIPID CUBIC PHASE) METHOD AT 4 DEGREES CELCIUS WITH THE 9.9 MONOACYLGLYCEROL (MONOOLEIN, 9.9 MAG) AS THE HOSTING LIPID.CRYSTALS WERE SOAKED WITH 5-10 MM AMPPCP, 60 MM ZINC ACETATE BEFORE HARVESTING. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03320, 1.28238 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 1, 2012 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→53.07 Å / Num. obs: 17218 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 68.67 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.9 | |||||||||
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.6 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZE5 Resolution: 2.701→53.075 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 29.62 / Stereochemistry target values: ML Details: THERE ARE THREE NCS-RELATED MOLECULES IN THE ASYMMETRIC UNIT BUT NCS GLOBAL 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: 92.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.701→53.075 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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