[English] 日本語
Yorodumi- PDB-3ze3: Crystal structure of the integral membrane diacylglycerol kinase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ze3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the integral membrane diacylglycerol kinase - delta7 | ||||||
Components | DIACYLGLYCEROL KINASE | ||||||
Keywords | TRANSFERASE / LIPID METABOLISM / IN MESO CRYSTALLISATION / LIPID CUBIC PHASE / LIPIDIC MESOPHASE / THERMOSTABLE MUTANT / MONOACYLGLYCEROL / 7.8 MAG | ||||||
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 / SAD / Resolution: 2.05 Å | ||||||
Authors | Li, D. / Pye, V.E. / Lyons, J.A. / Vogeley, L. / Aragao, D. / Caffrey, M. | ||||||
Citation | Journal: Nature / Year: 2013 Title: Crystal Structure of the Integral Membrane Diacylglycerol Kinase. Authors: Li, D. / Lyons, J.A. / Pye, V.E. / Vogeley, L. / Aragao, D. / Kenyon, C.P. / Shah, S.T.A. / Doherty, C. / Aherne, M. / Caffrey, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ze3.cif.gz | 253.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ze3.ent.gz | 208.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ze3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ze3_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ze3_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 3ze3_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3ze3_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/3ze3 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/3ze3 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) Description: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED ...Description: THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED MUTATIONS WERE MADE USING PCR. Plasmid: PTRCHISB_DGKA_DELTA7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): WH1061 / References: UniProt: P0ABN1, diacylglycerol kinase (ATP) |
---|
-Non-polymers , 7 types, 205 molecules
#2: Chemical | ChemComp-78N / ( #3: Chemical | ChemComp-78M / ( #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-FLC / | #6: Chemical | ChemComp-ACT / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Nonpolymer details | (2S)-2,3-DIHYDROXYPSequence details | THE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE ...THE CONSTRUCT CONTAINS AN N-TERMIANL HIS TAG 'GHHHHHHEL'. COMPARED TO THE WILDTYPE FORM, THE PROTEIN HAS SEVEN MUTATIONS. THEY ARE A41C, C46A, I53V, I70L, M96L, V107D AND C113A. | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 19 |
---|
-Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.86 % / Description: NONE |
---|---|
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, 0.06 M MAGNESIUM ACETATE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPIDIC CUBIC PHASE) METHOD AT 4 ...Details: 3-5 %(V/V) 2-METHYL-2, 4-PENTANEDIOL, 0.1 M SODIUM CHLORIDE, 0.06 M MAGNESIUM ACETATE, 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 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03320, 0.97944 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 13, 2012 / Details: K-B PAIR OF BIOMORPH MIRRORS | |||||||||
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.05→58.04 Å / Num. obs: 62716 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4 | |||||||||
Reflection shell | Resolution: 2.05→2.16 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.05→51.894 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 20.52 / Stereochemistry target values: ML Details: THE 6 CHAINS FORMING 2 TRIMERS PER ASYMMETRIC UNIT COULD BE RELATED BY NCS HOWEVER THIS WAS DETRIMENTAL TO REFINEMENT AND SO WAS NOT USED. FOR THE MAJORITY OF THE REFINEMENT THE PHASES FROM ...Details: THE 6 CHAINS FORMING 2 TRIMERS PER ASYMMETRIC UNIT COULD BE RELATED BY NCS HOWEVER THIS WAS DETRIMENTAL TO REFINEMENT AND SO WAS NOT USED. FOR THE MAJORITY OF THE REFINEMENT THE PHASES FROM SEMET DATA WERE USED, TARGET MLHL, UNTIL THE FINAL ROUNDS OF REFINEMENT WHERE TARGET WAS ML. THE FOLLOWING RESIDUES COULD NOT BE PLACED INTO ELECTRON DENSITY DUE TO DISORDER OR FLEXIBILITY - A1-5, B1-23, C1-31, D1-13, E1-35, E47-49, F1-33.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.383 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→51.894 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|