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Yorodumi- PDB-5ysp: Pyrophosphate-dependent kinase in the ribokinase family complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ysp | |||||||||
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Title | Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol | |||||||||
Components | TM0415 | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information PPi-dependent kinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Nagata, R. / Fujihashi, M. / Miki, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants. Authors: Nagata, R. / Fujihashi, M. / Sato, T. / Atomi, H. / Miki, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ysp.cif.gz | 224.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ysp.ent.gz | 178.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ysp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ysp_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5ysp_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5ysp_validation.xml.gz | 20.7 KB | Display | |
Data in CIF | 5ysp_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/5ysp ftp://data.pdbj.org/pub/pdb/validation_reports/ys/5ysp | HTTPS FTP |
-Related structure data
Related structure data | 5ysqC 1vk4S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 32104.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0415 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9WYP6 |
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-Non-polymers , 5 types, 100 molecules
#2: Chemical | #3: Chemical | ChemComp-MDN / | #4: Chemical | ChemComp-MG / | #5: Chemical | ChemComp-SO4 / | #6: 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: 1.99 Å3/Da / Density % sol: 38.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 4000, ammonium sulfate, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 54308 / % possible obs: 98.1 % / Redundancy: 3.3 % / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.7→1.73 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VK4 Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.561 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.106 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.113 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→50 Å
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Refine LS restraints |
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