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Yorodumi- PDB-6anh: Crystal structure of PPK2 class III in complex with Guanosine 5-t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6anh | ||||||
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Title | Crystal structure of PPK2 class III in complex with Guanosine 5-tetraphosphate | ||||||
Components | Polyphosphate:AMP phosphotransferase | ||||||
Keywords | TRANSFERASE / PPK2 / kinase / Guanosine 5-tetraphosphate | ||||||
Function / homology | Function and homology information Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / polyphosphate kinase activity / polyphosphate metabolic process Similarity search - Function | ||||||
Biological species | Cytophaga hutchinsonii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å | ||||||
Authors | Nocek, B. / Joachimiak, A. / Yakunin, A. | ||||||
Citation | Journal: Acs Catalysis / Year: 2018 Title: Structural Insights into Substrate Selectivity and Activity of Bacterial Polyphosphate Kinases Authors: Nocek, B. / Khusnutdinova, A.N. / Ruszkowski, M. / Flick, R. / Burda, M. / Batyrova, K. / Brown, G. / Mucha, A. / Joachimiak, A. / Berlicki, L. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6anh.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6anh.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 6anh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/an/6anh ftp://data.pdbj.org/pub/pdb/validation_reports/an/6anh | HTTPS FTP |
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-Related structure data
Related structure data | 6an9C 6angC 6aqeC 6aqnC 6au0C 6b18C 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 35539.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469) (bacteria) Strain: ATCC 33406 / NCIMB 9469 / Gene: CHU_0107 / Production host: Escherichia coli (E. coli) References: UniProt: Q11YW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor |
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#2: Chemical | ChemComp-BKP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.1 M Ammonium tartrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→36.2 Å / Num. obs: 17542 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.65→2.74 Å |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.65→36.17 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.719 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.255 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→36.17 Å
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Refine LS restraints |
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