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- PDB-1lny: Crystal structure of the recombinant mouse-muscle adenylosuccinat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lny | ||||||
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Title | Crystal structure of the recombinant mouse-muscle adenylosuccinate synthetase complexed with 6-phosphoryl-IMP, GDP and Mg | ||||||
![]() | Adenylosuccinate Synthetase | ||||||
![]() | LIGASE / Purine biosynthesis / GTP-binding | ||||||
Function / homology | ![]() Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity ...Purine ribonucleoside monophosphate biosynthesis / purine nucleotide metabolic process / adenylosuccinate synthase / adenylosuccinate synthase activity / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity / GTP binding / magnesium ion binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
![]() | ![]() Title: IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase. Authors: Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.3 KB | Display | ![]() |
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PDB format | ![]() | 147.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1iweC ![]() 1lonC ![]() 1looC ![]() 1j4bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer and it is contained by the asymmetric unit. |
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Components
#1: Protein | Mass: 50321.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.71 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 400, magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 IV / Detector: IMAGE PLATE / Date: Jul 20, 2001 / 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 | Resolution: 2.2→40.5 Å / Num. all: 50470 / Num. obs: 50176 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.2→2.29 Å / Redundancy: 3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2 / % possible all: 79 |
Reflection | *PLUS Num. obs: 48646 / % possible obs: 92.3 % / Num. measured all: 175127 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS Lowest resolution: 2.3 Å / % possible obs: 86.5 % / Rmerge(I) obs: 0.222 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1J4B Resolution: 2.2→5 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.32 Å / Rfactor Rfree error: 0.012
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Refinement | *PLUS Lowest resolution: 5 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.259 / Rfactor Rwork: 0.207 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.321 / Rfactor Rwork: 0.289 |