[English] 日本語
Yorodumi- PDB-1lvg: Crystal structure of mouse guanylate kinase in complex with GMP a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lvg | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of mouse guanylate kinase in complex with GMP and ADP | ||||||
Components | Guanylate kinase | ||||||
Keywords | TRANSFERASE / GMP kinase / Guanylate kinase | ||||||
Function / homology | Function and homology information dGDP biosynthetic process / dATP metabolic process / : / GDP biosynthetic process / glycoprotein transport / GDP-mannose metabolic process / Interconversion of nucleotide di- and triphosphates / guanylate kinase / dGMP metabolic process / GMP 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 / dGMP metabolic process / GMP metabolic process / purine nucleotide metabolic process / guanylate kinase activity / ATP metabolic process / photoreceptor inner segment / xenobiotic metabolic process / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sekulic, N. / Shuvalova, L. / Spangenberg, O. / Konrad, M. / Lavie, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural characterization of the closed conformation of mouse guanylate kinase. Authors: Sekulic, N. / Shuvalova, L. / Spangenberg, O. / Konrad, M. / Lavie, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1lvg.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1lvg.ent.gz | 40.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lvg ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lvg | HTTPS FTP |
---|
-Related structure data
Related structure data | 1ex7S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21947.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q64520, guanylate kinase |
---|---|
#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-ADP / |
#4: Chemical | ChemComp-5GP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.04 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EX7 Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.3 / Rfactor Rwork: 0.22 |