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Yorodumi- PDB-6h59: Crystal structure of Mycobacterium tuberculosis phosphatidylinosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h59 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis phosphatidylinositol phosphate synthase (PgsA1) with CDP-DAG bound | ||||||
Components | CDP-diacylglycerol--inositol 3-phosphatidyltransferase | ||||||
Keywords | TRANSFERASE / Phosphotransferase / Glycerophospholipid metabolism / Metal binding protein / Membrane protein | ||||||
Function / homology | Function and homology information CDP-diacylglycerol-inositol 3-phosphatidyltransferase activity / glycerophospholipid biosynthetic process / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phospholipid biosynthetic process / peptidoglycan-based cell wall / magnesium ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Grave, K. / Hogbom, M. | ||||||
Citation | Journal: Commun Biol / Year: 2019 Title: Structure ofMycobacterium tuberculosisphosphatidylinositol phosphate synthase reveals mechanism of substrate binding and metal catalysis. Authors: Grave, K. / Bennett, M.D. / Hogbom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h59.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h59.ent.gz | 139.9 KB | Display | PDB format |
PDBx/mmJSON format | 6h59.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6h59_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6h59_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6h59_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 6h59_validation.cif.gz | 27.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/6h59 ftp://data.pdbj.org/pub/pdb/validation_reports/h5/6h59 | HTTPS FTP |
-Related structure data
Related structure data | 6h53SC 6h5aC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23274.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: pgsA1, Rv2612c / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: P9WPG7, EC: 2.7.8.11 |
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-Non-polymers , 7 types, 163 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PGE / | #5: Chemical | #6: Chemical | ChemComp-OLB / ( #7: Chemical | ChemComp-1PE / | #8: 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: 2.75 Å3/Da / Density % sol: 55.33 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / pH: 6 Details: 33% PEG 400 (v/v), 0.1 M NaCl, 0.1 M Bis-Tris pH 6, and 0.1 M MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→74.61 Å / Num. obs: 48544 / % possible obs: 99.4 % / Redundancy: 12.8 % / Biso Wilson estimate: 17.25 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.7 / % possible all: 98.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6H53 Resolution: 1.8→49.62 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→49.62 Å
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Refine LS restraints |
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LS refinement shell |
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