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Yorodumi- PDB-1gin: CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gin | ||||||
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Title | CRYSTAL STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE FROM ESCHERICHIA COLI COMPLEXED WITH GDP, IMP, HADACIDIN, NO3-, AND MG2+. DATA COLLECTED AT 298K (PH 6.5). | ||||||
Components | ADENYLOSUCCINATE SYNTHETASE | ||||||
Keywords | LIGASE / PURINE NUCLEOTIDE BIOSYNTHESIS / GTP-HYDROLYZING 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: 2.8 Å | ||||||
Authors | Poland, B.W. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+. Authors: Poland, B.W. / 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 | 1gin.cif.gz | 123.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gin.ent.gz | 95.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gin_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1gin_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1gin_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 1gin_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/1gin ftp://data.pdbj.org/pub/pdb/validation_reports/gi/1gin | HTTPS FTP |
-Related structure data
-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 Details: GIFT FROM DR. B. BACHMAN (GENETIC CENTER, YALE UNIVERSITY) Source: (natural) Escherichia coli (E. coli) / Strain: PUR A STRAIN H1238 / References: UniProt: P0A7D4, adenylosuccinate synthase |
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-Non-polymers , 6 types, 167 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-NO3 / |
#4: Chemical | ChemComp-HDA / |
#5: Chemical | ChemComp-IMP / |
#6: Chemical | ChemComp-GDP / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: SIEMENS / Detector: AREA DETECTOR / Date: Feb 28, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 17336 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.094 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 128898 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å / % possible obs: 99 % |
-Processing
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Refinement | Resolution: 2.8→5 Å
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Displacement parameters | Biso mean: 30.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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