+Open data
-Basic information
Entry | Database: PDB / ID: 1j4b | ||||||
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Title | Recombinant Mouse-Muscle Adenylosuccinate Synthetase | ||||||
Components | adenylosuccinate synthetase | ||||||
Keywords | LIGASE / GTP-hydrolyzing enzymes / purine nucleotide cycle | ||||||
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: 2.5 Å | ||||||
Authors | Iancu, C.V. / Borza, T. / Choe, J.Y. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure. Authors: Iancu, C.V. / Borza, T. / Choe, J.Y. / 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 | 1j4b.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j4b.ent.gz | 73.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j4b_validation.pdf.gz | 411.2 KB | Display | wwPDB validaton report |
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Full document | 1j4b_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 1j4b_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1j4b_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j4/1j4b ftp://data.pdbj.org/pub/pdb/validation_reports/j4/1j4b | HTTPS FTP |
-Related structure data
Related structure data | 1sonS S: Starting model for refinement |
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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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-Components
#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) / Tissue: muscle / Cellular location: cytoplasm / Gene: Adss1 / Plasmid: pET28b / Species (production host): Escherichia coli / Cellular location (production host): cytoplasm / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28650, adenylosuccinate synthase |
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#2: 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: 2.4 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: Cacodylate 100 mM, pH6.5 PEG 8000 18% 200 mM Calcium Acetate | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 / 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 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: 2.5→39.6 Å / Num. obs: 16066 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2 / Rsym value: 0.224 / % possible all: 60 |
Reflection | *PLUS Num. measured all: 132963 |
Reflection shell | *PLUS % possible obs: 60 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SON Resolution: 2.5→39.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 132841.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.0352 Å2 / ksol: 0.357928 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→39.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 40.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / % reflection Rfree: 9.3 % / Rfactor Rwork: 0.265 |