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Yorodumi- PDB-2aj4: Crystal structure of Saccharomyces cerevisiae Galactokinase in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2aj4 | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae Galactokinase in complex with galactose and Mg:AMPPNP | ||||||
Components | Galactokinase | ||||||
Keywords | TRANSFERASE / galactokinase / galactosemia / transcription | ||||||
Function / homology | Function and homology information positive regulation of transcription by galactose / galactokinase / galactokinase activity / galactose catabolic process via UDP-galactose / carbohydrate phosphorylation / galactose metabolic process / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Thoden, J.B. / Sellick, C.A. / Timson, D.J. / Reece, R.J. / Holden, H.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Molecular structure of Saccharomyces cerevisiae Gal1p, a bifunctional galactokinase and transcriptional inducer Authors: Thoden, J.B. / Sellick, C.A. / Timson, D.J. / Reece, R.J. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2aj4.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2aj4.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 2aj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/2aj4 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/2aj4 | HTTPS FTP |
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-Related structure data
Related structure data | 2a2cS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 60364.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: GAL1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P04385, galactokinase #2: Sugar | |
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-Non-polymers , 4 types, 197 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG8000, LiCl, galactose, Mg:AMPPNP, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 6, 2005 / Details: montel |
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: 2.4→30 Å / Num. all: 44350 / Num. obs: 44350 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.075 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 4591 / Rsym value: 0.273 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A2C Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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