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Yorodumi- PDB-5wsa: Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wsa | |||||||||
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Title | Pyruvate kinase (PYK) from Mycobacterium tuberculosis in complex with Oxalate and allosteric activator Glucose 6-Phosphate | |||||||||
Components | Pyruvate kinase | |||||||||
Keywords | TRANSFERASE / pyruvate kinase / glycolysis / tetramer / allostery / synergism / phospho transferase | |||||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / glycolytic process / kinase activity / magnesium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | |||||||||
Authors | Zhong, W. / Cai, Q. / El Sahili, A. / Lescar, J. / Dedon, P.C. | |||||||||
Funding support | Singapore, 2items
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Citation | Journal: Nat Commun / Year: 2017 Title: Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis. Authors: Zhong, W. / Cui, L. / Goh, B.C. / Cai, Q. / Ho, P. / Chionh, Y.H. / Yuan, M. / Sahili, A.E. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. / Lescar, J. / Dedon, P.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wsa.cif.gz | 698.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wsa.ent.gz | 581.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/5wsa ftp://data.pdbj.org/pub/pdb/validation_reports/ws/5wsa | HTTPS FTP |
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-Related structure data
Related structure data | 5wrpSC 5ws8C 5ws9C 5wsbC 5wscC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 472 / Label seq-ID: 5 - 475
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 51014.336 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pyk, pykA, Rv1617, MTCY01B2.09 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WKE5, pyruvate kinase #2: Sugar | ChemComp-G6P / |
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-Non-polymers , 4 types, 184 molecules
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-OXL / #5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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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: 3.21 Å3/Da / Density % sol: 61.67 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 12% PEG 8000, 20% glycerol, 50 mM triethanolamine-HCl (TEA) buffer pH 7.2, 100 mM KCl, 50 mM MgCl2, 5 mM oxalate, 5 mM ATP, 5 mM D-Glucose 6-Phosphate. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | |||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 27, 2016 | |||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.85→62.71 Å / Num. obs: 59240 / % possible obs: 100 % / Redundancy: 5.6 % / Net I/σ(I): 13.7 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.85→2.93 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WRP Resolution: 2.85→62.71 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.765 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R Free: 0.061 / 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: 42.492 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→62.71 Å
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Refine LS restraints |
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