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Yorodumi- PDB-1xcf: Crystal structure of P28L/Y173F tryptophan synthase alpha-subunit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xcf | ||||||
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Title | Crystal structure of P28L/Y173F tryptophan synthase alpha-subunits from Escherichia coli | ||||||
Components | Tryptophan synthase alpha chain | ||||||
Keywords | LYASE / tryptophan synthase / a-subunits / E.coli / P28L/Y173F double mutants | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / aromatic amino acid family biosynthetic process / molecular adaptor activity / lyase activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Jang, S.B. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2004 Title: Structures of wild-type and P28L/Y173F tryptophan synthase alpha-subunits from Escherichia coli Authors: Jeong, M.S. / Jeong, J.K. / Lim, W.K. / Jang, S.B. #1: 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. / Seidel, 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 | 1xcf.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xcf.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 1xcf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xcf_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 1xcf_full_validation.pdf.gz | 450.5 KB | Display | |
Data in XML | 1xcf_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 1xcf_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/1xcf ftp://data.pdbj.org/pub/pdb/validation_reports/xc/1xcf | HTTPS FTP |
-Related structure data
Related structure data | 1xc4C 1k8xS 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: 28782.188 Da / Num. of mol.: 2 / Mutation: P28L/Y173F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: ptactrpAMK-M13 / Production host: Escherichia coli (E. coli) / Strain (production host): RB797 / References: UniProt: P0A877, tryptophan synthase #2: 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: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES-NA, isopropanol, polyethylene glycol4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 26, 2003 |
Radiation | Monochromator: copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 387319 / Num. obs: 48396 / % possible obs: 91.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 8 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.289 / Num. unique all: 3485 / % possible all: 79.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K8X Resolution: 1.8→30 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å
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