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Yorodumi- PDB-1lon: Crystal Structure of the Recombinant Mouse-Muscle Adenylosuccinat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lon | ||||||
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Title | Crystal Structure of the Recombinant Mouse-Muscle Adenylosuccinate Synthetase Complexed with 6-phosphoryl-IMP, GDP and Hadacidin | ||||||
Components | adenylosuccinate synthetase | ||||||
Keywords | LIGASE / Purine biosynthesis / GTP-binding | ||||||
Function / homology | Function and homology information 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 | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 1lon.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lon.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 1lon.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lon_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1lon_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1lon_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1lon_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lon ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lon | HTTPS FTP |
-Related structure data
Related structure data | 1iweC 1lnyC 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. The asymmetric unit contains one monomer. The other monomer is generated by the symmetry operation: -y, -x, 1/2-z. |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 50321.301 Da / Num. of mol.: 1 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 |
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-Non-polymers , 5 types, 190 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-IMO / |
#4: Chemical | ChemComp-HDA / |
#5: Chemical | ChemComp-GDP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, magnesium acetate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å |
Detector | Type: SBC-2 / Detector: CCD / Date: Apr 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 32291 / Num. obs: 31207 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3350 / % possible all: 90 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 32291 / % possible obs: 98.5 % / Num. measured all: 266913 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS Lowest resolution: 2.2 Å / % possible obs: 99.5 % / Rmerge(I) obs: 0.178 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J4B Resolution: 2.1→10 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015
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Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.224 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.315 / Rfactor Rwork: 0.313 |