+Open data
-Basic information
Entry | Database: PDB / ID: 1ig0 | ||||||
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Title | Crystal Structure of yeast Thiamin Pyrophosphokinase | ||||||
Components | Thiamin pyrophosphokinase | ||||||
Keywords | TRANSFERASE / Protein-substrate complex / compound active site / alpha-beta-alpha / beta sandwich | ||||||
Function / homology | Function and homology information Vitamin B1 (thiamin) metabolism / thiamine diphosphokinase / thiamine diphosphokinase activity / thiamine binding / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.8 Å | ||||||
Authors | Baker, L.-J. / Dorocke, J.A. / Harris, R.A. / Timm, D.E. | ||||||
Citation | Journal: Structure / Year: 2001 Title: The crystal structure of yeast thiamin pyrophosphokinase. Authors: Baker, L.J. / Dorocke, J.A. / Harris, R.A. / Timm, D.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ig0.cif.gz | 150.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ig0.ent.gz | 119.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ig0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ig0_validation.pdf.gz | 469.8 KB | Display | wwPDB validaton report |
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Full document | 1ig0_full_validation.pdf.gz | 484.1 KB | Display | |
Data in XML | 1ig0_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1ig0_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/1ig0 ftp://data.pdbj.org/pub/pdb/validation_reports/ig/1ig0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36659.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: THI80 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35202, thiamine diphosphokinase #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: 2.34 Å3/Da / Density % sol: 47.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: PEGMME 2000, ammonium sulfate, sodium acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 27, 1999 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.46 Å / Num. all: 61167 / Num. obs: 60988 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.8→1.91 Å / Rmerge(I) obs: 0.301 / % possible all: 80.3 |
Reflection | *PLUS Num. measured all: 303494 |
Reflection shell | *PLUS % possible obs: 74.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→29.46 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1842627.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.33 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.9 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28.6 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.339 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.301 |