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Yorodumi- PDB-1ofa: Crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-hep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofa | ||||||
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Title | Crystal structure of the tyrosine-regulated 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase from saccharomyces cerevisiae in complex with phosphoenolpyruvate and cobalt(ii) | ||||||
Components | PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE | ||||||
Keywords | LYASE / BETA-ALPHA-BARREL / AROMATIC AMINO-ACID BIOSYNTHESIS SYNTHASE / ALDOLASE / SYNTHETASE / MANGANESE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G.H. / Schneider, T.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism Authors: Koenig, V. / Pfeil, A. / 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 "BA" 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ofa.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofa.ent.gz | 115.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ofa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofa ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofa | HTTPS FTP |
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-Related structure data
Related structure data | 1oabC 1of8C 1ofbC 1ofoC 1ofpC 1ofqC 1ofrC 1hfbS 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: 39797.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: LIGAND\: PHOSPHOENOLPYRUVATE METAL\: COBALT(II) Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: RH1326 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32449, EC: 4.1.2.15 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 1.94 Å3/Da / Density % sol: 36.76 % |
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Crystal grow | pH: 8 Details: TRIS PH 7.5-9.0 10 MM 20% PEG3400, 5% GLYCEROL, 4 EQUIV. PEP, 2.5 EQUIV. CO2+ 13-17MG/ML DAHPS |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→18.6 Å / Num. obs: 128877 / % possible obs: 96.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.02→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.5 / % possible all: 86.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HFB Resolution: 2.02→17.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.162 / 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: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.18 Å2
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Refinement step | Cycle: LAST / Resolution: 2.02→17.57 Å
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Refine LS restraints |
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