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Yorodumi- PDB-6wmv: Structure of a phosphatidylinositol-phosphate synthase (PIPS) fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wmv | ||||||||||||
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Title | Structure of a phosphatidylinositol-phosphate synthase (PIPS) from Mycobacterium kansasii with evidence of substrate binding | ||||||||||||
Components | AfCTD-Phosphatidylinositol-phosphate synthase (PIPS) fusion | ||||||||||||
Keywords | MEMBRANE PROTEIN / CDP-alcohol phosphotransferase | ||||||||||||
Function / homology | Function and homology information phosphotransferase activity, for other substituted phosphate groups / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / magnesium ion binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Archaeoglobus fulgidus (archaea) Mycobacterium kansasii ATCC 12478 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.142 Å | ||||||||||||
Authors | Belcher Dufrisne, M. / Jorge, C.D. / Timoteo, C.G. / Petrou, V.I. / Ashraf, K.U. / Banerjee, S. / Clarke, O.B. / Santos, H. / Mancia, F. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Structural and Functional Characterization of Phosphatidylinositol-Phosphate Biosynthesis in Mycobacteria. Authors: Belcher Dufrisne, M. / Jorge, C.D. / Timoteo, C.G. / Petrou, V.I. / Ashraf, K.U. / Banerjee, S. / Clarke, O.B. / Santos, H. / Mancia, F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wmv.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wmv.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wmv_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 6wmv_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 6wmv_validation.xml.gz | 27.4 KB | Display | |
Data in CIF | 6wmv_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/6wmv ftp://data.pdbj.org/pub/pdb/validation_reports/wm/6wmv | HTTPS FTP |
-Related structure data
Related structure data | 6wm5C 4o6mS 5d91S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 40388.797 Da / Num. of mol.: 2 / Mutation: D17L,Q77L,G79S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea), (gene. exp.) Mycobacterium kansasii ATCC 12478 (bacteria) Gene: XD40_0003, XD48_0797, MKAN_26045 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) References: UniProt: A0A101DFK9, UniProt: U5WZP7, UniProt: O27985*PLUS |
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-Non-polymers , 10 types, 53 molecules
#2: Chemical | ChemComp-LIP / | ||||||||||||||||
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#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-TCE / | #5: Chemical | #6: Chemical | ChemComp-OLC / ( #7: Chemical | ChemComp-8K6 / #8: Chemical | #9: Chemical | ChemComp-C5P / | #10: Chemical | ChemComp-FLC / | #11: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 295 K / Method: lipidic cubic phase / pH: 6.1 Details: 100 mM NaCl, 100 mM Sodium Citrate, pH 6.1, 40 mM MgCl2, 29% PEG 400, 500 uM L-myo-inositol-1-phosphate (prepared in house), 2.5 mM CDP (Sigma) (precipitant). Concentrated protein at 30-35 ...Details: 100 mM NaCl, 100 mM Sodium Citrate, pH 6.1, 40 mM MgCl2, 29% PEG 400, 500 uM L-myo-inositol-1-phosphate (prepared in house), 2.5 mM CDP (Sigma) (precipitant). Concentrated protein at 30-35 mg/ml was mixed with monoolein at a 1:1.5 protein to lipid ratio |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2018 / Details: MD2 diffractometer |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.142→78.083 Å / Num. obs: 26006 / % possible obs: 58.72 % / Redundancy: 2 % / Biso Wilson estimate: 41.06 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.07329 / Rpim(I) all: 0.07329 / Rrim(I) all: 0.1036 / Net I/σ(I): 9.78 |
Reflection shell | Resolution: 2.142→2.221 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4034 / Mean I/σ(I) obs: 1.73 / Num. unique obs: 69 / CC1/2: 0.594 / CC star: 0.863 / Rpim(I) all: 0.4034 / Rrim(I) all: 0.5705 / % possible all: 1.57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5D91,4O6M Resolution: 2.142→78.083 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 36.47
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 116.15 Å2 / Biso mean: 45.381 Å2 / Biso min: 13.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.142→78.083 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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