[English] 日本語
![](img/lk-miru.gif)
- PDB-6ig2: Structure of mitochondrial CDP-DAG synthase Tam41 complexed with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ig2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, delta 74, F240A | |||||||||
![]() | Phosphatidate cytidylyltransferase, mitochondrial | |||||||||
![]() | TRANSFERASE / mitochondrial inner membrane / CDP-Diacylglycerol synthase / NTase fold | |||||||||
Function / homology | ![]() phosphatidate cytidylyltransferase / phosphatidate cytidylyltransferase activity / extrinsic component of mitochondrial inner membrane / CDP-diacylglycerol biosynthetic process / cardiolipin biosynthetic process / cardiolipin binding / phosphatidic acid binding / mitochondrial membrane organization / mitochondrial matrix / mitochondrion Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jiao, H.Z. / Yin, Y. / Liu, Z.F. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structures of the Mitochondrial CDP-DAG Synthase Tam41 Suggest a Potential Lipid Substrate Pathway from Membrane to the Active Site. Authors: Jiao, H. / Yin, Y. / Liu, Z. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 237.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 189.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 882.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 890 KB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 55.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ig4SC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 35856.719 Da / Num. of mol.: 4 / Mutation: F240A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: tam41, SPBC1A4.06c / Production host: ![]() ![]() References: UniProt: O74339, phosphatidate cytidylyltransferase #2: Chemical | ChemComp-CTP / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.53 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: evaporation, recrystallization Details: 0.1 M HEPES-Na, pH 7.5, 9% Tacsimate, pH 7.0, 2% PEG 3350, incubated with 10 mM MgCl2, 5 mM CTP for 1 h before crystallization PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 173.15 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 44684 / % possible obs: 100 % / Redundancy: 6.5 % / Rpim(I) all: 0.042 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4338 / Rpim(I) all: 0.482 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6IG4 Resolution: 2.882→47.604 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.92
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.882→47.604 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|