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Yorodumi- PDB-1og0: CRYSTAL STRUCTURE OF THE MUTANT G226S OF THE TYROSINE-REGULATED 3... -
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-Basic information
Entry | Database: PDB / ID: 1og0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE MUTANT G226S OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited | ||||||
Keywords | LYASE / BETA-ALPHA-BARREL | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G.H. / Schneider, T.R. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Mutant G226S of the Tyrosine-Regulated 3-Deoxy-D-Arabino-Heptulosonate -7-Phosphate Synthase from Saccharomyces Cerevisiae Complexed with Phenylalanine and Manganese Authors: Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G.H. / Schneider, T.R. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Evolution of Feedback-Inhibited Beta /Alpha Barrel Isoenzymes by Gene Duplication and a Single Mutation. Authors: Hartmann, M. / Schneider, T.R. / Pfeil, A. / Heinrich, G. / Lipscomb, W.N. / Braus, G.H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1og0.cif.gz | 508.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1og0.ent.gz | 418.4 KB | Display | PDB format |
PDBx/mmJSON format | 1og0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1og0 ftp://data.pdbj.org/pub/pdb/validation_reports/og/1og0 | HTTPS FTP |
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-Related structure data
Related structure data | 1hfbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39827.082 Da / Num. of mol.: 8 / Mutation: G226S Source method: isolated from a genetically manipulated source Details: LIGANDS PHENYLALANINE ION, MANGANESE Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: ARO4, YBR249C, YBR1701 / Production host: Saccharomyces cerevisiae (brewer's yeast) References: UniProt: P32449, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PHE / #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = ...CATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = PHOSPHOENO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | pH: 8 / Details: pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8463 / Wavelength: 0.8463 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8463 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→37 Å / Num. obs: 155910 / % possible obs: 91.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.69→2.8 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.5 / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HFB MOLECULE A Resolution: 2.7→29.83 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.0212 Å2 / ksol: 0.315139 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→29.83 Å
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Refine LS restraints |
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Xplor file |
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