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Yorodumi- PDB-1son: ADENYLOSUCCINATE SYNTHETASE IN COMPLEX WITH THE NATURAL FEEDBACK ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1son | ||||||
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Title | ADENYLOSUCCINATE SYNTHETASE IN COMPLEX WITH THE NATURAL FEEDBACK INHIBITOR AMP | ||||||
Components | ADENYLOSUCCINATE SYNTHETASEAdenylosuccinate synthase | ||||||
Keywords | LIGASE / PURINE NUCLEOTIDE BIOSYNTHESIS / GTP-HYDROLYZING ENZYME / HERBICIDE / SYNTHETASE | ||||||
Function / homology | Function and homology information adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding ...adenylosuccinate synthase / adenylosuccinate synthase activity / adenosine biosynthetic process / IMP metabolic process / 'de novo' AMP biosynthetic process / nucleobase-containing small molecule interconversion / purine nucleotide biosynthetic process / guanosine tetraphosphate binding / DNA damage response / GTP binding / magnesium ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / RIGID BODY REFINEMENT / Resolution: 2.55 Å | ||||||
Authors | Cowan-Jacob, S.W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: The mode of action and the structure of a herbicide in complex with its target: binding of activated hydantocidin to the feedback regulation site of adenylosuccinate synthetase. Authors: Fonne-Pfister, R. / Chemla, P. / Ward, E. / Girardet, M. / Kreuz, K.E. / Honzatko, R.B. / Fromm, H.J. / Schar, H.P. / Grutter, M.G. / Cowan-Jacob, S.W. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from Escherichia Coli Authors: Silva, M.M. / Poland, B.W. / Hoffman, C.R. / Fromm, H.J. / Honzatko, R.B. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Crystal Structure of Adenylosuccinate Synthetase from Escherichia Coli. Evidence for Convergent Evolution of GTP-Binding Domains Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M. / Honzatko, R.B. #3: Journal: J.Mol.Biol. / Year: 1988 Title: Preliminary X-Ray Crystallographic Study of Adenylosuccinate Synthetase from Escherichia Coli Authors: Serra, M.A. / Bass, M.B. / 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 | 1son.cif.gz | 85.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1son.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 1son.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/so/1son ftp://data.pdbj.org/pub/pdb/validation_reports/so/1son | HTTPS FTP |
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-Related structure data
Related structure data | 1sooSC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47269.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: PUR A STRAIN H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase |
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#2: Chemical | ChemComp-AMP / |
#3: Chemical | ChemComp-BME / |
#4: 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: 2.65 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.6 / Details: pH 8.6 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-25 ℃ / pH: 7.7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 13, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→28 Å / Num. obs: 17293 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.086 |
Reflection shell | Resolution: 2.55→2.62 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.4 / % possible all: 99.2 |
Reflection shell | *PLUS % possible obs: 99.2 % |
-Processing
Software |
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Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: 1SOO Resolution: 2.55→8 Å / σ(F): 0
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Displacement parameters | Biso mean: 34.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.55→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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