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Yorodumi- PDB-6au0: Crystal structure of PPK2 (Class III) in complex with bisphosphon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6au0 | ||||||
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Title | Crystal structure of PPK2 (Class III) in complex with bisphosphonate inhibitor (2-((3,5-dichlorophenyl)amino)ethane-1,1-diyl)diphosphonic acid | ||||||
Components | Polyphosphate:AMP phosphotransferase | ||||||
Keywords | transferase/transferase inhibitor / PPK2 / kinase / bisphosphonate inhibitor / TRANSFERASE / transferase-transferase inhibitor complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nocek, B. / Ruszkowski, M. / Joachimiak, A. / Berlicki, L. / 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 | 6au0.cif.gz | 142.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6au0.ent.gz | 111.6 KB | Display | PDB format |
PDBx/mmJSON format | 6au0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6au0_validation.pdf.gz | 891.6 KB | Display | wwPDB validaton report |
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Full document | 6au0_full_validation.pdf.gz | 893.7 KB | Display | |
Data in XML | 6au0_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 6au0_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/6au0 ftp://data.pdbj.org/pub/pdb/validation_reports/au/6au0 | HTTPS FTP |
-Related structure data
Related structure data | 6an9C 6angC 6anhC 6aqeC 6aqnC 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: 35577.523 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 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q11YW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor | ||
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#2: Chemical | ChemComp-BWJ / {[( | ||
#3: Chemical | #4: 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: 3.78 Å3/Da / Density % sol: 67.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 0.1 M Phosphate Citrate pH 4.2 40% PEG 300 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2014 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 32073 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.1→2.141 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 1588 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→93.42 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.818 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.139 / 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: 55.396 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→93.42 Å
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Refine LS restraints |
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