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Yorodumi- PDB-6qxl: Crystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qxl | ||||||
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Title | Crystal Structure of Pyruvate Kinase II (PykA) from Pseudomonas aeruginosa in complex with sodium malonate, magnesium and glucose-6-phosphate | ||||||
Components | Pyruvate kinase | ||||||
Keywords | TRANSFERASE / Pyruvate kinase / PykA / homotetramer / polypeptide / G6P-bound / PykA-MLI-Mg complex | ||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.43 Å | ||||||
Authors | Abdelhamid, Y. / Brear, P. / Welch, M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Evolutionary plasticity in the allosteric regulator-binding site of pyruvate kinase isoform PykA fromPseudomonas aeruginosa. Authors: Abdelhamid, Y. / Brear, P. / Greenhalgh, J. / Chee, X. / Rahman, T. / Welch, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qxl.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6qxl.ent.gz | 918.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qxl_validation.pdf.gz | 12.9 MB | Display | wwPDB validaton report |
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Full document | 6qxl_full_validation.pdf.gz | 12.9 MB | Display | |
Data in XML | 6qxl_validation.xml.gz | 219.5 KB | Display | |
Data in CIF | 6qxl_validation.cif.gz | 303.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/6qxl ftp://data.pdbj.org/pub/pdb/validation_reports/qx/6qxl | HTTPS FTP |
-Related structure data
Related structure data | 4hyvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 24 molecules ABCDEFGHIJKL
#1: Protein | Mass: 52325.930 Da / Num. of mol.: 12 / Fragment: Polypeptide Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: pykA, pyk, pykA_1, C8257_26620, CAZ10_21690, DZ940_08845, NCTC13719_04679, PAERUG_E15_London_28_01_14_03018, PAMH19_3832, RW109_RW109_05666 Plasmid: pET19m / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A069PYA5, UniProt: Q9HW72*PLUS, pyruvate kinase #2: Sugar | ChemComp-G6P / |
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-Non-polymers , 4 types, 2295 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-MLI / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.1 Å3/Da / Density % sol: 60.33 % / Mosaicity: 0 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 % PEG 3350, 0.1 M Bis-Tris propane pH 7.5, 0.2 M disodium malonate, 20 mM MgCl2, 2 mM G6P and 2 mM PEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9159 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.43→405.44 Å / Num. obs: 292996 / % possible obs: 100 % / Redundancy: 14.7 % / Biso Wilson estimate: 45.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.038 / Rrim(I) all: 0.148 / Net I/σ(I): 11.1 / Num. measured all: 4318494 / Scaling rejects: 4029 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HYV Resolution: 2.43→158.03 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.37 / SU Rfree Blow DPI: 0.242 / SU Rfree Cruickshank DPI: 0.243
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Displacement parameters | Biso max: 235.94 Å2 / Biso mean: 55.44 Å2 / Biso min: 19.03 Å2
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Refinement step | Cycle: final / Resolution: 2.43→158.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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