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Yorodumi- PDB-5l6v: Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5l6v | |||||||||
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Title | Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a negative allosteric regulator adenosine monophosphate (AMP) - AGPase*AMP | |||||||||
Components | Glucose-1-phosphate adenylyltransferase | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | Function and homology information glucose-1-phosphate adenylyltransferase complex / glucose-1-phosphate adenylyltransferase / glucose-1-phosphate adenylyltransferase activity / glycogen biosynthetic process / AMP binding / protein homotetramerization / magnesium ion binding / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.667 Å | |||||||||
Authors | Cifuente, J.O. / Albesa-Jove, D. / Comino, N. / Madariaga-Marcos, J. / Agirre, J. / Lopez-Fernandez, S. / Garcia-Alija, M. / Guerin, M.E. | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Basis of Glycogen Biosynthesis Regulation in Bacteria. Authors: Cifuente, J.O. / Comino, N. / Madariaga-Marcos, J. / Lopez-Fernandez, S. / Garcia-Alija, M. / Agirre, J. / Albesa-Jove, D. / Guerin, M.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5l6v.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5l6v.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5l6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5l6v_validation.pdf.gz | 7.9 MB | Display | wwPDB validaton report |
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Full document | 5l6v_full_validation.pdf.gz | 7.9 MB | Display | |
Data in XML | 5l6v_validation.xml.gz | 227.9 KB | Display | |
Data in CIF | 5l6v_validation.cif.gz | 310.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/5l6v ftp://data.pdbj.org/pub/pdb/validation_reports/l6/5l6v | HTTPS FTP |
-Related structure data
Related structure data | 5l6sC 1yp2S 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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-Components
#1: Protein | Mass: 48758.590 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: glgC, b3430, JW3393 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P0A6V1, glucose-1-phosphate adenylyltransferase #2: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #3: Chemical | ChemComp-AMP / #4: Chemical | ChemComp-PO4 / | #5: 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: 2.58 Å3/Da / Density % sol: 52.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10mM EDTA, 10% D-(+)-Sucrose, 50mM MgCl2, 5mM ADP, 16% (w/v) PEG 10000, 100mM Imidazole pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.667→45.271 Å / Num. obs: 224803 / % possible obs: 100 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.64 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.69 |
Reflection shell | Resolution: 2.667→2.762 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.7832 / Mean I/σ(I) obs: 1.74 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YP2 Resolution: 2.667→45.271 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 28.2 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.667→45.271 Å
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Refine LS restraints |
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LS refinement shell |
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