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Yorodumi- PDB-1kfc: CRYSTAL STRUCTURE OF ALPHAT183V MUTANT OF TRYPTOPHAN SYNTHASE FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kfc | ||||||
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Title | CRYSTAL STRUCTURE OF ALPHAT183V MUTANT OF TRYPTOPHAN SYNTHASE FROM SALMONELLA TYPHIMURIUM With Indole Propanol Phosphate | ||||||
Components | (TRYPTOPHAN SYNTHASE ...) x 2 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 1kfc.cif.gz | 152.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kfc.ent.gz | 114.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/1kfc ftp://data.pdbj.org/pub/pdb/validation_reports/kf/1kfc | HTTPS FTP |
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-Related structure data
Related structure data | 1k8xC 1kfbC 1kfeC 1kfjC 1kfkC 1qopS C: citing same article (ref.) S: Starting model for refinement |
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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
-TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB
#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 details: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42918.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Plasmid details: PSTB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 674 molecules
#3: Chemical | ChemComp-IPL / |
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#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-PLP / |
#6: 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: 2.55 Å3/Da / Density % sol: 51.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.45→91.3 Å / Num. all: 127862 / Num. obs: 122217 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.6 Å2 |
Reflection shell | Resolution: 1.45→1.5 Å / % possible all: 91.1 |
Reflection | *PLUS Num. measured all: 312863 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS % possible obs: 91.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1qop Resolution: 1.5→19.99 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2078283.84 / Data cutoff high rms absF: 2078283.84 / 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: 53.2452 Å2 / ksol: 0.390057 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.33 |