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Yorodumi- PDB-1lny: Crystal structure of the recombinant mouse-muscle adenylosuccinat... -
+Open data
-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 | ||||||
Components | Adenylosuccinate SynthetaseAdenylosuccinate synthase | ||||||
Keywords | LIGASE / Purine biosynthesis / GTP-binding | ||||||
Function / homology | Function and homology information Purine ribonucleoside monophosphate biosynthesis / AMP biosynthetic process / adenylosuccinate synthase / adenylosuccinate synthase activity / purine nucleotide metabolic process / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding ...Purine ribonucleoside monophosphate biosynthesis / AMP biosynthetic process / adenylosuccinate synthase / adenylosuccinate synthase activity / purine nucleotide metabolic process / aspartate metabolic process / IMP metabolic process / 'de novo' AMP biosynthetic process / AMP salvage / actin filament binding / GTPase activity / GTP binding / magnesium ion binding / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Iancu, C.V. / Borza, T. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lny.cif.gz | 188.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lny.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/1lny ftp://data.pdbj.org/pub/pdb/validation_reports/ln/1lny | HTTPS FTP |
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-Related structure data
Related structure data | 1iweC 1lonC 1looC 1j4bS 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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Details | The biological assembly is a dimer and it is contained by the asymmetric unit. |
-Components
#1: Protein | Mass: 50321.301 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: ADSS1 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P28650, adenylosuccinate synthase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |