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Yorodumi- PDB-1ofr: CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofr | ||||||
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Title | CRYSTAL STRUCTURE 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 | ||||||
Keywords | LYASE / BETA-ALPHA-BARREL / AROMATIC AMINO-ACID BIOSYNTHESIS | ||||||
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. / 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. / Heinrich, G. / Braus, G. / Schneider, T.R. | ||||||
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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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. DETERMINATION METHOD: DSSP 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 | 1ofr.cif.gz | 511.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofr.ent.gz | 421.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ofr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofr ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofr | HTTPS FTP |
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-Related structure data
Related structure data | 1oabC 1of8C 1ofaC 1ofbC 1ofoC 1ofpC 1ofqC 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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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Details | THE 8 MOLECULES CONTAINED IN THE ASSYMETRIC UNIT AREARRANGED IN TWO TETRAMERS (DIMER OF DIMERS) WITH APPROXIMATE 222 POINT SYMMETRY. THE TETRAMERS HAVE VERY SIMILAR ORIENTATIONS,WITH THEIR CENTERS OF MASS BEING RELATED BY A CRYSTALLOGRAPHIC TRANSLATION OF (0.5,0.5,0) |
-Components
#1: Protein | Mass: 39797.055 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: LIGANDS ARE PHENYLALANINE ION, MANGANESE 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: 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: 2.25 Å3/Da / Density % sol: 45.22 % |
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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 |
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: 47 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: MOLECULE A OF PDB-CODE 1HFB Resolution: 2.7→37.2 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 813855.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE EFFECTOR PHENYLALANINE IS MODELLED ONLY IN THE FOUR MOLECULES C, D, G, H
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 18.0698 Å2 / ksol: 0.2985 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→37.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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