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- PDB-1lvg: Crystal structure of mouse guanylate kinase in complex with GMP a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lvg | ||||||
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Title | Crystal structure of mouse guanylate kinase in complex with GMP and ADP | ||||||
![]() | Guanylate kinase | ||||||
![]() | TRANSFERASE / GMP kinase / Guanylate kinase | ||||||
Function / homology | ![]() dGDP biosynthetic process / dATP metabolic process / : / GDP biosynthetic process / glycoprotein transport / GDP-mannose metabolic process / Interconversion of nucleotide di- and triphosphates / guanylate kinase / purine nucleotide metabolic process / dGMP metabolic process ...dGDP biosynthetic process / dATP metabolic process / : / GDP biosynthetic process / glycoprotein transport / GDP-mannose metabolic process / Interconversion of nucleotide di- and triphosphates / guanylate kinase / purine nucleotide metabolic process / dGMP metabolic process / GMP metabolic process / guanylate kinase activity / ATP metabolic process / photoreceptor inner segment / xenobiotic metabolic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sekulic, N. / Shuvalova, L. / Spangenberg, O. / Konrad, M. / Lavie, A. | ||||||
![]() | ![]() Title: Structural characterization of the closed conformation of mouse guanylate kinase. Authors: Sekulic, N. / Shuvalova, L. / Spangenberg, O. / Konrad, M. / Lavie, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.5 KB | Display | ![]() |
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PDB format | ![]() | 40.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ex7S 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: 21947.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-5GP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Details: protein solution: 10 mg/ml mGMPK, 2mM GMP, 2mM ADP and 5mM MgCl2 reservoir solution: 38-46% PEG 4000, 0.1M Na-citrate pH 5.6, 0.1-0.2 M ammonium acetate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. obs: 14942 / % possible obs: 98.4 % / Num. measured all: 105017 / Rmerge(I) obs: 0.121 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 5.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EX7 Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3 / Rfactor Rwork: 0.22 |