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Yorodumi- PDB-1juy: REFINED CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1juy | ||||||
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Title | REFINED CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH HYDANTOCIDIN 5'-PHOSPHATE GDP, HPO4(2-), MG2+, AND HADACIDIN | ||||||
Components | ADENYLOSUCCINATE SYNTHETASE | ||||||
Keywords | LIGASE / PURINE BIOSYNTHESIS / GTP-BINDING / GTP-HYDROLYSING ENZYMES | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Poland, B.W. / Lee, S.-F. / Subramanian, M.V. / Siehl, D.L. / Anderson, R.J. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin. Authors: Poland, B.W. / Lee, S.F. / Subramanian, M.V. / Siehl, D.L. / Anderson, R.J. / Fromm, H.J. / Honzatko, R.B. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Refined Crystal Structures of Unligated Adenylosuccinate Synthetase from E.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 E.Coli Authors: Poland, B.W. / Silva, M.M. / Serra, M.A. / Cho, Y. / Kim, K.H. / Harris, E.M. / 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 | 1juy.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1juy.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 1juy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1juy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1juy_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1juy_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 1juy_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1juy ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1juy | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#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 (A GIFT FROM DR. B. BACHMAN (GENETIC CENTER, YALE UNIVERSITY)) References: UniProt: P0A7D4, adenylosuccinate synthase |
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-Non-polymers , 6 types, 238 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-PI / |
#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-H5P / |
#6: Chemical | ChemComp-HDA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.65 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jul 4, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 22503 / % possible obs: 99 % / Redundancy: 6 % / Rmerge(I) obs: 0.094 |
Reflection | *PLUS Highest resolution: 2.6 Å / Num. measured all: 181667 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 93 % |
-Processing
Software |
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Refinement | Resolution: 2.5→5 Å
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Displacement parameters | Biso mean: 22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.25 / Highest resolution: 2.6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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