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Yorodumi- PDB-1kfb: CRYSTAL STRUCTURE OF ALPHAT183V MUTANT OF TRYPTOPHAN SYNTHASE FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kfb | ||||||
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Title | CRYSTAL STRUCTURE OF ALPHAT183V MUTANT OF TRYPTOPHAN SYNTHASE FROM SALMONELLA TYPHIMURIUM WITH Indole Glycerol Phosphate | ||||||
Components |
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Keywords | LYASE / HELIX | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Kulik, V. / Weyand, M. / Siedel, R. / Niks, D. / Arac, D. / Dunn, M.F. / Schlichting, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: On the Role of alphaTHR183 in the Allosteric Regulation and Catalytic Mechanism of Tryptophan Synthase Authors: Kulik, V. / Weyand, M. / Siedel, R. / Niks, D. / Arac, D. / Dunn, M.F. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kfb.cif.gz | 141.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kfb.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 1kfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/1kfb ftp://data.pdbj.org/pub/pdb/validation_reports/kf/1kfb | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28696.824 Da / Num. of mol.: 1 / Mutation: T183V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00929 |
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#2: Protein | Mass: 42787.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1 |
#3: Chemical | ChemComp-IGP / |
#4: Chemical | ChemComp-PLP / |
#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: 2.56 Å3/Da / Density % sol: 52.01 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 8000, EDTA, spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→91.3 Å / Num. all: 57355 / Num. obs: 57355 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 9.9 Å2 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 79.6 |
Reflection | *PLUS Num. obs: 54830 / Num. measured all: 153263 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 79.6 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Resolution: 1.9→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2221550.76 / Data cutoff high rms absF: 2221550.76 / 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: 67.4153 Å2 / ksol: 0.412936 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 2 Å |