[English] 日本語
Yorodumi- PDB-5ld1: Crystal Structure of Polyphosphate Kinase from Meiothermus ruber ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ld1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP | |||||||||
Components | Polyphosphate:AMP phosphotransferase | |||||||||
Keywords | TRANSFERASE / Polyphosphate Kinase | |||||||||
Function / homology | Function and homology information phosphotransferase activity, phosphate group as acceptor / polyphosphate metabolic process / kinase activity Similarity search - Function | |||||||||
Biological species | Meiothermus ruber (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.09 Å | |||||||||
Authors | Gerhardt, S. / Einsle, O. / Kemper, F. / Schwarzer, N. | |||||||||
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. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ld1.cif.gz | 479.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ld1.ent.gz | 388.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ld1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ld1 ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ld1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5lc9SC 5lcdC 5ldbC 5ll0C 5llbC 5llfC 5maqC 5o6kC 5o6mC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-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.) Meiothermus ruber (bacteria) / Gene: MrH_2468 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S7ASE9 |
---|
-Non-polymers , 5 types, 895 molecules
#2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.44 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
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: 2.09→168.01 Å / Num. obs: 80333 / % possible obs: 100 % / Redundancy: 18.4 % / Biso Wilson estimate: 29.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.26 / Rsym value: 0.264 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.09→2.21 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.586 / Mean I/σ(I) obs: 2.4 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | R rigid body: 0.595
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LC9 Resolution: 2.09→118.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.148
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.57 Å2 / Biso mean: 32.44 Å2 / Biso min: 10.03 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→118.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.09→2.14 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|