+Open data
-Basic information
Entry | Database: PDB / ID: 1a48 | ||||||
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Title | SAICAR SYNTHASE | ||||||
Components | PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE | ||||||
Keywords | ATP BINDING PROTEIN / PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYNTHASE / PURINE BIOSYNTHESIS | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolesuccinocarboxamide synthase / phosphoribosylaminoimidazolesuccinocarboxamide synthase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.9 Å | ||||||
Authors | Levdikov, V.M. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K.S. | ||||||
Citation | Journal: Structure / Year: 1998 Title: The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis. Authors: Levdikov, V.M. / Barynin, V.V. / Grebenko, A.I. / Melik-Adamyan, W.R. / Lamzin, V.S. / Wilson, K.S. #1: Journal: Biokhimiia / Year: 1992 Title: [Substrate Specificity of Phosphoribosyl-Aminoimidazole-Succinocarboxyamide Synthetase (Saicar-Synthetase) from Saccharomyces Cerevisiae Yeast] (Russian) Authors: Alenin, V.V. / Ostanin, K.V. / Kostikova, T.R. / Domkin, V.D. / Zubova, V.A. / Smirnov, M.N. #2: Journal: J.Mol.Biol. / Year: 1992 Title: Crystallization and Preliminary X-Ray Investigation of Phosphoribosylaminoimidazolesuccinocarboxamide Synthase from the Yeast Saccharomyces Cerevisiae Authors: Grebenko, A.I. / Levdikov, V.M. / Barynin, V.V. / Melik-Adamyan, W.R. / Myasnikov, A.N. #3: Journal: Prog.Nucleic Acid Res.Mol.Biol. / Year: 1992 Title: De Novo Purine Nucleotide Biosynthesis Authors: Zalkin, H. / Dixon, J.E. #4: Journal: Gene / Year: 1991 Title: The Saccharomyces Cerevisiae Ade1 Gene: Structure, Overexpression and Possible Regulation by General Amino Acid Control Authors: Myasnikov, A.N. / Sasnauskas, K.V. / Janulaitis, A.A. / Smirnov, M.N. #5: Journal: Biokhimiia / Year: 1989 Title: [Isolation and Properties of Phosphoribosyl-Aminoimidazole-Succinocarboxyamide-Synthetase from Saccharomyces Cerevisiae Yeasts] (Russian) Authors: Ostanin, K.V. / Alenin, V.V. / Domkin, V.D. / Smirnov, M.N. #6: Journal: Bioorg.Khim. / Year: 1986 Title: [Nucleotide Sequence of the Ade 1 Gene of the Yeast Saccharomyces Cerevisiae] (Russian) Authors: Miasnikov, A.N. / Plavnik, Iu.A. / Sasnauskas, K.V. / Gedminene, G.K. / Ianulaitis, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a48.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a48.ent.gz | 60.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a48_validation.pdf.gz | 430.8 KB | Display | wwPDB validaton report |
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Full document | 1a48_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 1a48_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 1a48_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a48 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a48 | 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
#1: Protein | Mass: 34545.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: GRF18 References: UniProt: P27616, phosphoribosylaminoimidazolesuccinocarboxamide synthase | ||
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#2: Chemical | #3: 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: 45 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1991 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→10 Å / Num. obs: 24879 / % possible obs: 97 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7 / % possible all: 95 |
Reflection shell | *PLUS % possible obs: 95 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 1.9→10 Å / σ(F): 0 Details: THE LAST CYCLES OF REFINEMENT INCLUDED THE PARTIAL CONTRIBUTION FROM HYDROGEN ATOMS PLACED AT THEIR IDEALISED POSITIONS WHICH RESULTED IN IMPROVEMENT OF THE R FACTOR BY ABOUT 0.010.
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Displacement parameters | Biso mean: 23.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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