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Yorodumi- PDB-1adi: STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE AT PH 6.5 AND 25 DEGREES... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1adi | ||||||
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Title | STRUCTURE OF ADENYLOSUCCINATE SYNTHETASE AT PH 6.5 AND 25 DEGREES CELSIUS | ||||||
Components | ADENYLOSUCCINATE SYNTHETASE | ||||||
Keywords | LIGASE / PURINE NUCLEOTIDE BIOSYNTHESIS / GTP-HYDROLYZING ENZYME | ||||||
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 | Silva, M.M. / Poland, B.W. / Hoffman, C.M. / Fromm, H.J. / Honzatko, R.B. | ||||||
Citation | 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. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1adi.cif.gz | 232 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1adi.ent.gz | 189.6 KB | Display | PDB format |
PDBx/mmJSON format | 1adi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1adi_validation.pdf.gz | 379.2 KB | Display | wwPDB validaton report |
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Full document | 1adi_full_validation.pdf.gz | 408.1 KB | Display | |
Data in XML | 1adi_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1adi_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/1adi ftp://data.pdbj.org/pub/pdb/validation_reports/ad/1adi | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98902, 0.01348, -0.14717), Vector: |
-Components
#1: Protein | Mass: 47269.598 Da / Num. of mol.: 2 / 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 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.34 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / 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 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. obs: 104085 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Num. obs: 32170 / Num. measured all: 104085 |
-Processing
Software |
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Refinement | Resolution: 2.5→5 Å / σ(F): 0 Details: THERE ARE TWO REGIONS THAT ARE DISORDERED CONSISTING OF RESIDUES 121 - 130 AND 298 - 303.
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Displacement parameters | Biso mean: 25.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 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' / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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