+Open data
-Basic information
Entry | Database: PDB / ID: 5ck7 | ||||||
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Title | Mouse ADP-dependent Glucokinase; AMP bound | ||||||
Components | ADP-dependent glucokinaseADP-specific glucokinase | ||||||
Keywords | TRANSFERASE / ADPGK / ribokinase / kinase / AMP | ||||||
Function / homology | Function and homology information ADP-specific glucose/glucosamine kinase / ADP-specific glucokinase activity / Glycolysis / glycolytic process / glucose metabolic process / phosphorylation / endoplasmic reticulum / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.99 Å | ||||||
Authors | Richter, J.P. / Ronimus, R.S. / Sutherland-Smith, A.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: The Structural and Functional Characterization of Mammalian ADP-dependent Glucokinase. Authors: Richter, J.P. / Goroncy, A.K. / Ronimus, R.S. / Sutherland-Smith, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ck7.cif.gz | 191.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ck7.ent.gz | 150.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ck7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/5ck7 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/5ck7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ccfSC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53067.738 Da / Num. of mol.: 1 / Fragment: UNP residues 51-495 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Adpgk / Plasmid: pBAD-TOPO / Production host: Escherichia coli (E. coli) References: UniProt: Q8VDL4, ADP-specific glucose/glucosamine kinase |
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#2: Chemical | ChemComp-AMP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.59 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion Details: Seeding of preequilibrated drops of 0.2 M NH4Cl, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→39.64 Å / Num. all: 9031 / Num. obs: 9031 / % possible obs: 97.1 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.99→3.1 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 80.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5CCF Resolution: 2.99→39.64 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.897 / SU B: 44.368 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / 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: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.723 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→39.64 Å
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