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Yorodumi- PDB-3qv6: Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qv6 | ||||||
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Title | Crystal structure of Leishmania mexicana pyruvate kinase(LmPYK)in complex with acid blue 80. | ||||||
Components | Pyruvate kinase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Pyruvate kinase / glycolysis / tim barrel / sugar kinase / ADP/ATP binding / cytosol / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / cellular response to insulin stimulus / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania mexicana (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Morgan, H.P. / Auld, D.S. / McNae, I.W. / Nowicki, M.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The trypanocidal drug suramin and other trypan blue mimetics are inhibitors of pyruvate kinases and bind to the adenosine site. Authors: Morgan, H.P. / McNae, I.W. / Nowicki, M.W. / Zhong, W. / Michels, P.A. / Auld, D.S. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qv6.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qv6.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 3qv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qv6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3qv6_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3qv6_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 3qv6_validation.cif.gz | 45.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qv6 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qv6 | HTTPS FTP |
-Related structure data
Related structure data | 3pp7C 3qv7C 3qv8C 3qv9C 1pklS S: Starting model for refinement 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: 54467.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania mexicana (eukaryote) / Strain: BEL46 / Gene: PYK / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q27686, pyruvate kinase #2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 7-16% PEG 8,000, 20 mM TEA buffer (pH 7.2), 50 mM MgCl2, 100 mM KCl and 10-25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å | |||||||||||||||
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 2.85→86.08 Å / Num. all: 181103 / Num. obs: 39558 / % possible obs: 100 % / Observed criterion σ(F): 2.85 / Observed criterion σ(I): 2.85 / Redundancy: 4.6 % / Biso Wilson estimate: 77.4 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.094 / Net I/σ(I): 11.8 | |||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 4.5 % / % possible all: 100
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-Processing
Software | Name: REFMAC / Version: 5.5.0109 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PKL Resolution: 2.85→86.08 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.085 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.567 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→86.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.852→2.926 Å / Total num. of bins used: 20
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