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Open data
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Basic information
Entry | Database: PDB / ID: 5o6k | ||||||
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Title | Structure of Polyphosphate Kinase from Meiothermus ruber N121D | ||||||
![]() | Polyphosphate:AMP phosphotransferase | ||||||
![]() | TRANSFERASE / Polyphosphate Kinase type 2 class III | ||||||
Function / homology | ![]() Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / phosphotransferase activity, phosphate group as acceptor / polyphosphate metabolic process / kinase activity / phosphorylation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kemper, F. / Gerhardt, S. / Einsle, O. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 432.9 KB | Display | ![]() |
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PDB format | ![]() | 360.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.8 KB | Display | ![]() |
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Full document | ![]() | 494.5 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lc9SC ![]() 5lcdC ![]() 5ld1C ![]() 5ldbC ![]() 5ll0C ![]() 5llbC ![]() 5llfC ![]() 5maqC ![]() 5o6mC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31607.961 Da / Num. of mol.: 4 / Mutation: N121D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 100 mM Tris/HCl pH 8.5 27 % (w/v) PEG 3350 200 mM Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 9, 2017 / Details: MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→47.91 Å / Num. obs: 30049 / % possible obs: 99.9 % / Redundancy: 14 % / CC1/2: 0.997 / Rmerge(I) obs: 0.317 / Rpim(I) all: 0.083 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 14.3 % / Rmerge(I) obs: 1.709 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4310 / CC1/2: 0.774 / Rpim(I) all: 0.447 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LC9 Resolution: 2.903→47.91 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.63 / 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: 2.903→47.91 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -42.2016 Å / Origin y: 0.3619 Å / Origin z: 9.8445 Å
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Refinement TLS group | Selection details: all |