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Yorodumi- PDB-3tqk: Structure of Phospho-2-dehydro-3-deoxyheptonate aldolase from Fra... -
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-Basic information
Entry | Database: PDB / ID: 3tqk | ||||||
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Title | Structure of Phospho-2-dehydro-3-deoxyheptonate aldolase from Francisella tularensis SCHU S4 | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
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 / metal ion binding Similarity search - Function | ||||||
Biological species | Francisella tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Franklin, M.C. / Cheung, J. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. Authors: Chaudhury, S. / Abdulhameed, M.D. / Singh, N. / Tawa, G.J. / D'haeseleer, P.M. / Zemla, A.T. / Navid, A. / Zhou, C.E. / Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Love, J. / Graf, J.F. / ...Authors: Chaudhury, S. / Abdulhameed, M.D. / Singh, N. / Tawa, G.J. / D'haeseleer, P.M. / Zemla, A.T. / Navid, A. / Zhou, C.E. / Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Love, J. / Graf, J.F. / Rozak, D.A. / Dankmeyer, J.L. / Amemiya, K. / Daefler, S. / Wallqvist, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tqk.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tqk.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 3tqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tqk_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
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Full document | 3tqk_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 3tqk_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 3tqk_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/3tqk ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tqk | HTTPS FTP |
-Related 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: 38359.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Strain: tularensis / Gene: aroG, FTT_0963c / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q5NG89, 3-deoxy-7-phosphoheptulonate synthase |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M imidazole, 0.26 M Ca acetate, 9.14% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 15, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→73.34 Å / Num. all: 20297 / Num. obs: 20258 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.09 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3 / Num. unique all: 979 / Rsym value: 0.498 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 12.36 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.207 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.321 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.9802 Å / Origin y: 25.3965 Å / Origin z: 17.1806 Å
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