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Yorodumi- PDB-7e4l: Conversion of pyrophosphate-dependent myo-inositol-1 kinase into ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7e4l | ||||||
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Title | Conversion of pyrophosphate-dependent myo-inositol-1 kinase into myo-inositol-3 kinase by N78L/S89L mutation | ||||||
Components | PfkB domain-containing protein | ||||||
Keywords | TRANSFERASE / pyrophosphate-dependent kinase | ||||||
Function / homology | PPi-dependent kinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase-like / METHYLENEDIPHOSPHONIC ACID / PfkB domain-containing protein Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Tashiro, R. / Miki, K. / Fujihashi, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Altering the Phosphorylation Position of Pyrophosphate-Dependent myo -Inositol-1-Kinase Based on Its Crystal Structure. Authors: Tashiro, R. / Sato, T. / Atomi, H. / Miki, K. / Fujihashi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e4l.cif.gz | 124.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e4l.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 7e4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/7e4l ftp://data.pdbj.org/pub/pdb/validation_reports/e4/7e4l | HTTPS FTP |
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-Related structure data
Related structure data | 5yspS S: Starting model for refinement |
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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: 32129.789 Da / Num. of mol.: 2 / Mutation: N78L/S89L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Gene: Tmari_0412 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / References: UniProt: R4NYE9 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.03 Å3/Da / Density % sol: 39.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 26% (w/v) poly(ethylene glycol) 4000, 2mM ammonium sulfate, 100mM sodium acetate buffer (pH 5.4) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 43707 / % possible obs: 62.5 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rrim(I) all: 0.051 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 9.1 / Num. unique obs: 4684 / CC1/2: 0.985 / Rrim(I) all: 0.134 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5ysp Resolution: 1.6→42.65 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.558 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→42.65 Å
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