+Open data
-Basic information
Entry | Database: PDB / ID: 6ig4 | |||||||||
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Title | Structure of mitochondrial CDP-DAG synthase Tam41, delta 74 | |||||||||
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 / phosphatidic acid binding / cardiolipin binding / mitochondrial membrane organization / mitochondrial matrix / mitochondrion Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.261 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 | 6ig4.cif.gz | 129.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ig4.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ig4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ig4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6ig4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6ig4_validation.xml.gz | 24 KB | Display | |
Data in CIF | 6ig4_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/6ig4 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/6ig4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35932.812 Da / Num. of mol.: 2 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 | #3: Chemical | ChemComp-PT / #4: 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: 2.4 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% Tacsimate, pH 7.0, 20 mM CdCl2, 10 mM K2Pt(CN)4 |
-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: 0.978 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 32658 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.26→2.3 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 1605 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.261→34.677 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.261→34.677 Å
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Refine LS restraints |
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LS refinement shell |
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