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Yorodumi- PDB-2cnu: Atomic resolution structure of SAICAR-synthase from Saccharomyces... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cnu | ||||||
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Title | Atomic resolution structure of SAICAR-synthase from Saccharomyces cerevisiae complexed with aspartic acid | ||||||
Components | PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE | ||||||
Keywords | LIGASE / PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYN LIGASE / ACETYLATION / ATP BINDING PROTEIN / 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 / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Urusova, D.V. / Antonyuk, S.V. / Grebenko, A.I. / Levdikov, V.M. / Barynin, V.V. / Popov, A.N. / Lamzin, V.S. / Melik-Adamyan, W.R. | ||||||
Citation | Journal: To be Published Title: Saicar Synthase: Substrate Recognition, Conformational Flexibility and Catalysis. Authors: Urusova, D.V. / Antonyuk, S.V. / Grebenko, A.I. / Levdikov, V.M. / Barynin, V.V. / Popov, A.N. / Lamzin, V.S. / Melik-Adamyan, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cnu.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cnu.ent.gz | 147.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/2cnu ftp://data.pdbj.org/pub/pdb/validation_reports/cn/2cnu | HTTPS FTP |
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-Related structure data
Related structure data | 2cnqC 1a48S 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
#1: Protein | Mass: 34545.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) References: UniProt: P27616, phosphoribosylaminoimidazolesuccinocarboxamide synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 2.1 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | pH: 7.5 Details: TRIS-HCL BUFFER, PH 7.5, ASPARTIC ACID, AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→24 Å / Num. obs: 131992 / % possible obs: 94.4 % / Redundancy: 4 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.05→1.08 Å / Redundancy: 4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A48 Resolution: 1.05→23.97 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.854 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→23.97 Å
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Refine LS restraints |
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