+Open data
-Basic information
Entry | Database: PDB / ID: 2cnv | ||||||
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Title | SAICAR-synthase from Saccharomyces cerevisiae complexed SAICAR | ||||||
Components | PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE | ||||||
Keywords | LIGASE / PHOSPHORIBOSYLAMINOIMIDAZOLESUCCINOCARBOXAMIDE (SAICAR) SYN LIGASE / SYNTHETASE / ACETYLATION / ATPBINDING 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: 2 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, V.R. | ||||||
Citation | Journal: Crystallogr.Rep.(Transl. Kristallografiya) / Year: 2006 Title: X-Ray Diffraction Study of the Complex of the Enzyme Saicar Synthase with the Reaction Product Authors: Urusova, D.V. / Levdikov, V.M. / Antonyuk, S.V. / Grebenko, A.I. / Lamzin, V.S. / Melik-Adamyan, V.R. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cnv.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cnv.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/2cnv ftp://data.pdbj.org/pub/pdb/validation_reports/cn/2cnv | HTTPS FTP |
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-Related structure data
Related structure data | 1a48S S: Starting model for refinement |
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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-SSS / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE CONFLICT IN THE RECORDS BELOW HAS BEEN DESCRIBED IN REFERENCES WITH PUBMED ID=1658741, 7941740 ...THE CONFLICT IN THE RECORDS BELOW HAS BEEN DESCRIBED IN REFERENCES | |
-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: 41.5 % |
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Crystal grow | pH: 7.5 Details: AMMONIUM SULPHATE, ASPARTIC ACID, TRIS-HCL BUFFER, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 273 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: MIRROS |
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: 2→24.4 Å / Num. obs: 20692 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 7.7 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A48 Resolution: 2→23.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.875 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.186 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2→23.95 Å
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