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Yorodumi- PDB-1ofq: CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofq | ||||||
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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 MANGANESE(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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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. / Pfeil, A. / Heinrich, G. / Lipscomb, W. / Braus, G. | ||||||
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. 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ofq.cif.gz | 270.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofq.ent.gz | 215.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ofq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofq ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofq | HTTPS FTP |
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-Related structure data
Related structure data | 1oabC 1of8C 1ofaC 1ofbC 1ofoC 1ofpC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39797.055 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: METAL ION\: MANGANESE(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 | ChemComp-MN / #3: 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: 2.72 Å3/Da / Density % sol: 54.85 % |
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Crystal grow | Temperature: 277 K / pH: 8 Details: TRIS PH 7.5-9.0 10 MM 20% PEG3400, 2.4 EQUIV. MN, 13-17MG/ML DAHPS, 4 DEGREE |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.8 Å / Num. obs: 68895 / % possible obs: 99.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 13.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HFB Resolution: 2.7→19.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1011482.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 28.3231 Å2 / ksol: 0.323403 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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