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Yorodumi- PDB-1k8y: CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k8y | ||||||
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Title | CRYSTAL STRUCTURE OF THE TRYPTOPHAN SYNTHASE BETA-SER178PRO MUTANT COMPLEXED WITH D,L-ALPHA-GLYCEROL-3-PHOSPHATE | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Weyand, M. / Schlichting, I. / Marabotti, A. / Mozzarelli, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of the beta Ser178--> Pro mutant of tryptophan synthase. A "knock-out" allosteric enzyme. Authors: Weyand, M. / Schlichting, I. / Herde, P. / Marabotti, A. / Mozzarelli, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k8y.cif.gz | 156 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k8y.ent.gz | 117 KB | Display | PDB format |
PDBx/mmJSON format | 1k8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k8y_validation.pdf.gz | 477.5 KB | Display | wwPDB validaton report |
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Full document | 1k8y_full_validation.pdf.gz | 524.2 KB | Display | |
Data in XML | 1k8y_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 1k8y_validation.cif.gz | 54.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/1k8y ftp://data.pdbj.org/pub/pdb/validation_reports/k8/1k8y | HTTPS FTP |
-Related structure data
Related structure data | 1k7xC 1k8zC 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 on special symmetry positions |
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-Components
-TRYPTOPHAN SYNTHASE ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28698.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P00929, tryptophan synthase |
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#2: Protein | Mass: 42797.723 Da / Num. of mol.: 1 / Mutation: S178P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: TRPA/TRPB / Plasmid: PSTB7 / Production host: Escherichia coli (E. coli) / Strain (production host): CB149 / References: UniProt: P0A2K1, tryptophan synthase |
-Non-polymers , 4 types, 661 molecules
#3: Chemical | ChemComp-13P / |
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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: 2.6 Å3/Da / Density % sol: 52.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: pH 7.80 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 11, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.6 Å / Num. obs: 111900 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 2.991 % / Rsym value: 0.078 / Net I/σ(I): 9.76 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 2.045 % / Mean I/σ(I) obs: 2.93 / Rsym value: 0.246 / % possible all: 91 |
Reflection | *PLUS Highest resolution: 1.5 Å / Observed criterion σ(I): -3 / Num. measured all: 289431 / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 91 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 2.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QOP Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 22.526 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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