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- PDB-5ldb: Crystal Structure of Polyphosphate Kinase from Meiothermus ruber ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ldb | ||||||
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Title | Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP | ||||||
![]() | Polyphosphate:AMP phosphotransferase | ||||||
![]() | TRANSFERASE / Polyphosphate Kinase | ||||||
Function / homology | ![]() phosphotransferase activity, phosphate group as acceptor / polyphosphate metabolic process / kinase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gerhardt, S. / Einsle, O. / Kemper, F. / Schwarzer, N. | ||||||
![]() | ![]() 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 | ![]() | 471.7 KB | Display | ![]() |
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PDB format | ![]() | 385.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5lc9SC ![]() 5lcdC ![]() 5ld1C ![]() 5ll0C ![]() 5llbC ![]() 5llfC ![]() 5maqC ![]() 5o6kC ![]() 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33778.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 500 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % / Mosaicity: 0.08 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 14, 2015 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.75 Å / Num. obs: 59190 / % possible obs: 100 % / Redundancy: 27 % / Biso Wilson estimate: 38.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.47 / Rsym value: 0.488 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 28.2 % / Rmerge(I) obs: 4.798 / Mean I/σ(I) obs: 1.1 / Rsym value: 4.97 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LC9 Resolution: 2.3→47.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.279 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.192
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Displacement parameters | Biso max: 205.86 Å2 / Biso mean: 48.35 Å2 / Biso min: 11.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→47.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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