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Yorodumi- PDB-1ay0: IDENTIFICATION OF CATALYTICALLY IMPORTANT RESIDUES IN YEAST TRANS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ay0 | ||||||
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Title | IDENTIFICATION OF CATALYTICALLY IMPORTANT RESIDUES IN YEAST TRANSKETOLASE | ||||||
Components | TRANSKETOLASE | ||||||
Keywords | TRANSFERASE / TRANSKETOLASE MECHANISM / THIAMIN DIPHOSPHATE / MUTANT / KETONE RESIDUES | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER METHODS / Resolution: 2.6 Å | ||||||
Authors | Wikner, C. / Nilsson, U. / Meshalkina, L. / Udekwu, C. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Identification of catalytically important residues in yeast transketolase. Authors: Wikner, C. / Nilsson, U. / Meshalkina, L. / Udekwu, C. / Lindqvist, Y. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ay0.cif.gz | 261.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ay0.ent.gz | 210.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ay0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ay0_validation.pdf.gz | 500.6 KB | Display | wwPDB validaton report |
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Full document | 1ay0_full_validation.pdf.gz | 522.8 KB | Display | |
Data in XML | 1ay0_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 1ay0_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ay0 ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ay0 | HTTPS FTP |
-Related structure data
Related structure data | 1trkS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.784, 0.001, -0.621), Vector: |
-Components
#1: Protein | Mass: 73820.320 Da / Num. of mol.: 2 / Mutation: H263A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: H402 / Gene: TKL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23254, transketolase #2: Chemical | #3: Chemical | |
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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: 2.37 Å3/Da / Density % sol: 48.11 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: SEE PAPER SCHNEIDER ET AL., (1989), J. BIOL. CHEM. 264,21619-21620, pH 7.5 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop / Details: Schneider, G., (1989) J. Biol. Chem., 264, 21619. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→25 Å / Num. obs: 36959 / % possible obs: 82.7 % / Observed criterion σ(I): 1 / Redundancy: 10.3 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.215 / Rsym value: 0.215 / % possible all: 65.1 |
Reflection | *PLUS Num. measured all: 380321 |
Reflection shell | *PLUS % possible obs: 65.1 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER METHODS Starting model: PDB ENTRY 1TRK Resolution: 2.6→5.5 Å / Rfactor Rfree error: 0.014 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→5.5 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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