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- PDB-3vpz: Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vpz | ||||||
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Title | Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A | ||||||
![]() | Glucokinase | ||||||
![]() | TRANSFERASE / GLUCOKINASE / COLD-ADAPTED | ||||||
Function / homology | ![]() glucokinase / glucokinase activity / D-glucose binding / glycolytic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oda, T. / Fuchita, N. / Motoshima, H. / Kawamoto, M. / Watanabe, K. | ||||||
![]() | ![]() Title: Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A Authors: Oda, T. / Fuchita, N. / Motoshima, H. / Kawamoto, M. / Watanabe, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78.2 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.8 KB | Display | ![]() |
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Full document | ![]() | 433.3 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q18S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 35131.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M Trimethylamine N-oxide dihydrate, 20% PEGMME 2000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 31, 2011 |
Radiation | Monochromator: Si(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→19.39 Å / Num. obs: 36190 / % possible obs: 95.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.3 |
Reflection shell | Highest resolution: 1.69 Å / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Q18 Resolution: 1.69→18.56 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.54 / SU ML: 0.084 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.076 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→18.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.734 Å / Total num. of bins used: 20
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