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Yorodumi- PDB-6ig2: Structure of mitochondrial CDP-DAG synthase Tam41 complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ig2 | |||||||||
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Title | Structure of mitochondrial CDP-DAG synthase Tam41 complexed with CTP, delta 74, F240A | |||||||||
Components | Phosphatidate cytidylyltransferase, mitochondrial | |||||||||
Keywords | TRANSFERASE / mitochondrial inner membrane / CDP-Diacylglycerol synthase / NTase fold | |||||||||
Function / homology | Function and homology information 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 | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.882 Å | |||||||||
Authors | Jiao, H.Z. / Yin, Y. / Liu, Z.F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Structure / Year: 2019 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ig2.cif.gz | 237.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ig2.ent.gz | 189.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ig2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/6ig2 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/6ig2 | HTTPS FTP |
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-Related structure data
Related structure data | 6ig4SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35856.719 Da / Num. of mol.: 4 / Mutation: F240A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: tam41, SPBC1A4.06c / Production host: Escherichia coli (E. coli) References: UniProt: O74339, phosphatidate cytidylyltransferase #2: Chemical | ChemComp-CTP / | #3: Water | ChemComp-HOH / | |
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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: 3.37 Å3/Da / Density % sol: 63.53 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.977 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.882→47.604 Å
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Refine LS restraints |
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LS refinement shell |
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