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Yorodumi- PDB-8zly: Crystal structure of Streptococcus pneumoniae pyruvate kinase in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8zly | ||||||
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Title | Crystal structure of Streptococcus pneumoniae pyruvate kinase in complex with oxalate and fructose 1,6-bisphosphate and UDP | ||||||
Components | Pyruvate kinase | ||||||
Keywords | TRANSFERASE / Pyruvate kinase / Streptococcus pneumoniae / Glycolysis | ||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Streptococcus pneumoniae R6 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Nakashima, R. / Taguchi, A. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2024 Title: Structural basis of nucleotide selectivity in pyruvate kinase. Authors: Taguchi, A. / Nakashima, R. / Nishino, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zly.cif.gz | 864.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zly.ent.gz | 700.9 KB | Display | PDB format |
PDBx/mmJSON format | 8zly.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zly_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 8zly_full_validation.pdf.gz | 5.6 MB | Display | |
Data in XML | 8zly_validation.xml.gz | 178.3 KB | Display | |
Data in CIF | 8zly_validation.cif.gz | 262.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/8zly ftp://data.pdbj.org/pub/pdb/validation_reports/zl/8zly | HTTPS FTP |
-Related structure data
Related structure data | 8xw6C 8xw7C 8xw8C 8xw9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 16 molecules ABCDEFGH
#1: Protein | Mass: 56993.590 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: pykF / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQ84 #2: Sugar | ChemComp-FBP / |
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-Non-polymers , 5 types, 3887 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-UDP / #5: Chemical | ChemComp-K / #6: Chemical | ChemComp-OXL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 60 mM HEPES pH7.3, 75 mM NaCl, 75 mM KCl, 10 mM MgCl2, 75 mM Na formate, 14 % PEG3350, 10 mM oxalate, 10 mM FBP, 5 mM UDP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2023 Details: Main beamline optics is a double-crystal monochromator and a horizontal focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.89→48.17 Å / Num. obs: 423736 / % possible obs: 99.8 % / Redundancy: 13.34 % / CC1/2: 0.996 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.079 / Net I/σ(I): 6.23 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→48.16 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.116 / 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: 36.73 Å2
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Refinement step | Cycle: 1 / Resolution: 1.89→48.16 Å
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Refine LS restraints |
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