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Yorodumi- PDB-2tys: CRYSTAL STRUCTURES OF MUTANT (BETAK87T) TRYPTOPHAN SYNTHASE ALPHA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2tys | ||||||
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Title | CRYSTAL STRUCTURES OF MUTANT (BETAK87T) TRYPTOPHAN SYNTHASE ALPHA2 BETA2 COMPLEX WITH LIGANDS BOUND TO THE ACTIVE SITES OF THE ALPHA AND BETA SUBUNITS REVEAL LIGAND-INDUCED CONFORMATIONAL CHANGES | ||||||
Components | (TRYPTOPHAN SYNTHASE) x 2 | ||||||
Keywords | LYASE / CARBON-OXYGEN LYASE / TRYPTOPHAN BIOSYNTHESIS / PYRIDOXAL PHOSPHATE | ||||||
Function / homology | Function and homology information tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / ISOMORPHOUS WITH PDB ENTRY 1WSY. / Resolution: 1.9 Å | ||||||
Authors | Rhee, S. / Parris, K.D. / Hyde, C.C. / Ahmed, S.A. / Miles, E.W. / Davies, D.R. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Crystal structures of a mutant (betaK87T) tryptophan synthase alpha2beta2 complex with ligands bound to the active sites of the alpha- and beta-subunits reveal ligand-induced conformational changes. Authors: Rhee, S. / Parris, K.D. / Hyde, C.C. / Ahmed, S.A. / Miles, E.W. / Davies, D.R. #1: Journal: J.Biol.Chem. / Year: 1993 Title: Lysine 87 in the Beta Subunit of Tryptophan Synthase that Forms an Internal Aldimine with Pyridoxal Phosphate Serves Critical Roles in Transimination, Catalysis, and Product Release Authors: Lu, Z. / Nagata, S. / Mcphie, P. / Miles, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tys.cif.gz | 142.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tys.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 2tys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2tys_validation.pdf.gz | 769.7 KB | Display | wwPDB validaton report |
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Full document | 2tys_full_validation.pdf.gz | 777.5 KB | Display | |
Data in XML | 2tys_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 2tys_validation.cif.gz | 42 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/2tys ftp://data.pdbj.org/pub/pdb/validation_reports/ty/2tys | 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: 28698.797 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T Source method: isolated from a genetically manipulated source Details: L-TRYPTOPHAN BOUND TO THE BETA SUBUNIT IN A FORM OF SCHIFF BASE WITH COENZYME PYRIDOXAL 5'-PHOSPHATE Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42960.922 Da / Num. of mol.: 1 / Mutation: CHAIN B, K87T Source method: isolated from a genetically manipulated source Details: L-TRYPTOPHAN BOUND TO THE BETA SUBUNIT IN A FORM OF SCHIFF BASE WITH COENZYME PYRIDOXAL 5'-PHOSPHATE Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cell line: CB149 / Gene: TRPA/TRPB / Plasmid: PSTB7 / Cell line (production host): CB149 / Gene (production host): TRPA/TRPB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A2K1, tryptophan synthase |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PLT / [ |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 50MM NABICINE (PH 7.8), 1MM NA-EDTA, 0.8-1.5MM SPERMINE, 12% PEG8000 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / Details: pH is adjusted to 7.8 with NaOH | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1992 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.9 Å / Num. obs: 50490 / % possible obs: 84.6 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 3.7 / % possible all: 46.8 |
Reflection shell | *PLUS % possible obs: 46.8 % |
-Processing
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1WSY. Resolution: 1.9→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 29.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor obs: 0.171 / Rfactor Rfree: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |