+Open data
-Basic information
Entry | Database: PDB / ID: 8eq0 | |||||||||
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Title | Escherichia coli pyruvate kinase G381A | |||||||||
Components | Pyruvate kinase | |||||||||
Keywords | TRANSFERASE / Pyruvate kinase / Long term evolution experiment / Kinase | |||||||||
Function / homology | Function and homology information pyruvate kinase / pyruvate kinase activity / potassium ion binding / kinase activity / phosphorylation / magnesium ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | |||||||||
Authors | Donovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Beneficial mutations occurring in E. coli pyruvate kinase afford new allosteric mechanisms leading to faster resumption of growth Authors: Donovan, K.A. / Coombes, D. / Dobson, R.C.J. / Cooper, T.F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eq0.cif.gz | 323.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eq0.ent.gz | 268.4 KB | Display | PDB format |
PDBx/mmJSON format | 8eq0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eq0_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 8eq0_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 8eq0_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 8eq0_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/8eq0 ftp://data.pdbj.org/pub/pdb/validation_reports/eq/8eq0 | HTTPS FTP |
-Related structure data
Related structure data | 8edqC 8edrC 8edsC 8edtC 8eq1C 8eq3C 8eu4C 4yngS S: Starting model for refinement 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50806.352 Da / Num. of mol.: 2 / Mutation: G381A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: EL79_2019, EL80_2048 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A0G552, pyruvate kinase #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.95 Å3/Da / Density % sol: 58.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M (0.2M DL-Glutamic acid monohydrate; 0.2M DL-Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine), 0.1M (1.0M Sodium HEPES; 1.0M MOPS (acid)), 30% v/v (40% v/v Glycerol; 20% w/v PEG 4000) |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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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: Oct 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→48.09 Å / Num. obs: 35719 / % possible obs: 97.76 % / Redundancy: 7.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.1913 / Net I/σ(I): 7.11 |
Reflection shell | Resolution: 2.62→2.716 Å / Mean I/σ(I) obs: 1.78 / Num. unique obs: 2799 / CC1/2: 0.515 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YNG Resolution: 2.62→48.09 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 23.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.09 Å2 / Biso mean: 31.6102 Å2 / Biso min: 11.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.62→48.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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