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Yorodumi- PDB-4yeg: Characterisation of Polyphosphate Kinase 2 from the Intracellular... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yeg | ||||||
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Title | Characterisation of Polyphosphate Kinase 2 from the Intracellular Pathogen Francisella tularensis | ||||||
Components | Polyphosphate kinase 2 | ||||||
Keywords | TRANSFERASE / polyphosphate kinase enzyme | ||||||
Function / homology | Function and homology information phosphorus metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Francisella tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Parnell, A.E. / Roach, P.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biosci.Rep. / Year: 2016 Title: Biochemical and structural characterization of polyphosphate kinase 2 from the intracellular pathogen Francisella tularensis. Authors: Batten, L.E. / Parnell, A.E. / Wells, N.J. / Murch, A.L. / Oyston, P.C. / Roach, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yeg.cif.gz | 229.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yeg.ent.gz | 183 KB | Display | PDB format |
PDBx/mmJSON format | 4yeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yeg_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 4yeg_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 4yeg_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 4yeg_validation.cif.gz | 60.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yeg ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yeg | HTTPS FTP |
-Related structure data
Related structure data | 3czqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32963.930 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) Gene: ppk2, DR80_1140, DR81_590, DR84_1109, DR85_1285, DR86_904, DR87_59 Production host: Escherichia coli (E. coli) References: UniProt: A0A080S703, UniProt: Q5NEQ5*PLUS, ATP-polyphosphate phosphotransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.8 M Na Citrate, 0.1 M Na HEPES, 2.5 mM AMP-PNP, 1 mM MgCl2 |
-Data collection
Diffraction | Mean temperature: 273.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→81.65 Å / Num. obs: 61793 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.23→2.29 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.539 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CZQ Resolution: 2.23→76.638 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→76.638 Å
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Refine LS restraints |
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LS refinement shell |
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