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Yorodumi- PDB-1v7y: Crystal structure of tryptophan synthase alpha-subunit from Esche... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v7y | ||||||
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Title | Crystal structure of tryptophan synthase alpha-subunit from Escherichia coli at room temperature | ||||||
Components | Tryptophan synthase alpha chain | ||||||
Keywords | LYASE / tryptophan synthase / tryptophan / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nishio, K. / Morimoto, Y. / Ishizuka, M. / Ogasahara, K. / Yutani, K. / Tsukihara, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Conformational Changes in the alpha-Subunit Coupled to Binding of the beta(2)-Subunit of Tryptophan Synthase from Escherichia coli: Crystal Structure of the Tryptophan Synthase alpha-Subunit Alon Authors: Nishio, K. / Morimoto, Y. / Ishizuka, M. / Ogasahara, K. / Tsukihara, T. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v7y.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v7y.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 1v7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/1v7y ftp://data.pdbj.org/pub/pdb/validation_reports/v7/1v7y | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28752.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: puc8pTrpA, trpA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A877, tryptophan synthase #2: Chemical | #3: 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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Ammonium sulfate, Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Jul 1, 1994 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.56 Å / Num. obs: 15954 / % possible obs: 89.8 % / Biso Wilson estimate: 35.8 Å2 |
Reflection shell | Resolution: 2.5→2.66 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.56 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 312267.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.5551 Å2 / ksol: 0.355914 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.56 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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