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Yorodumi- PDB-1oab: CRYSTAL STRUCTURE OF THE TYROSINE REGULATED 3-DEOXY-D-ARABINO-HEP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1oab | ||||||
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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 MANGANESE(II) | ||||||
Components | TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE | ||||||
Keywords | LYASE / BETA-ALPHA-BARREL / SYNTHASE | ||||||
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: 1.9 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. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 8-STRANDED BARRELS. THESE ARE 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 | 1oab.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oab.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 1oab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oab_validation.pdf.gz | 455.4 KB | Display | wwPDB validaton report |
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Full document | 1oab_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 1oab_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1oab_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oab ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oab | HTTPS FTP |
-Related structure data
Related structure data | 1of8C 1ofaC 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 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: 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: 36.7 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: TRIS PH 7.5-9.0 10 MM, 20% PEG3400, 5% GLYCEROL, 4 EQUIV. PEP, 13-17MG/ML DAHPS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 9 / PH range high: 7.5 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Jul 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: 1.9→20 Å / Num. obs: 178093 / % possible obs: 99.3 % / Redundancy: 3.63 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.34 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.9 / % possible all: 97.5 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 19.9 Å / Num. obs: 48773 / Num. measured all: 178093 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS % possible obs: 96.9 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HFB Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.969 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.98 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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