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Yorodumi- PDB-5llf: Structure of Polyphosphate Kinase 2 mutant D117N from Francisella... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5llf | ||||||
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Title | Structure of Polyphosphate Kinase 2 mutant D117N from Francisella tularensis with polyphosphate | ||||||
Components | Polyphosphate kinase 2 | ||||||
Keywords | TRANSFERASE / Polyphosphate kinase / polyphosphate metabolism / nucleotide metabolism | ||||||
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 subsp. tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Roach, P.L. / Parnell, A.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures. Authors: Parnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. / Einsle, O. / Oyston, P.C.F. / Andexer, J.N. / Roach, P.L. #1: 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 | 5llf.cif.gz | 237.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5llf.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 5llf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5llf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5llf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5llf_validation.xml.gz | 40.9 KB | Display | |
Data in CIF | 5llf_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/5llf ftp://data.pdbj.org/pub/pdb/validation_reports/ll/5llf | HTTPS FTP |
-Related structure data
Related structure data | 5lc9C 5lcdC 5ld1C 5ldbC 5ll0C 5llbC 5maqC 5o6kC 5o6mC 4yegS 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, 4 molecules ABCD
#1: Protein | Mass: 32134.059 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria) Gene: ppk2, FTT_1564, BZ14_1190 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q5NEQ5, ATP-polyphosphate phosphotransferase |
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-Non-polymers , 6 types, 257 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-6YX / [ | #4: Chemical | ChemComp-6YY / | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-6YW / [ | #7: 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: 3.01 Å3/Da / Density % sol: 59.16 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 32.5 % MPD/PEG100/PEG3350, 0.1 M Bicine/Trizma base pH 8.5, 0.09 M NPS, 0.5 mM polyP, 2.5 mM AMPPCH2P |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→69.57 Å / Num. obs: 68434 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 13 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YEG Resolution: 2.31→69.5 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2.31→69.5 Å
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