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Open data
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Basic information
Entry | Database: PDB / ID: 1g69 | ||||||
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Title | THIAMIN PHOSPHATE SYNTHASE | ||||||
![]() | THIAMIN PHOSPHATE SYNTHASE | ||||||
![]() | TRANSFERASE / THIAMIN BIOSYNTHESIS / TIM BARREL | ||||||
Function / homology | ![]() thiamine phosphate synthase / thiamine-phosphate diphosphorylase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Peapus, D.H. / Chiu, H.-J. / Campobasso, N. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. | ||||||
![]() | ![]() Title: Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase. Authors: Peapus, D.H. / Chiu, H.J. / Campobasso, N. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. #1: ![]() Title: Crystal Structure of Thiamin Phosphate Synthase from Bacillus subtilis at 1.25A Resolution Authors: Chiu, H.-J. / Reddick, J.J. / Begley, T.P. / Ealick, S.E. #2: ![]() Title: CHARACTERIZATION OF THE BACILLUS SUBTILIS THIC OPERON INVOLVED IN THIAMINE BIOSYNTHESIS Authors: ZHANG, Y. / TAYLOR, S.V. / CHIU, H.-J. / BEGLEY, T.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.4 KB | Display | ![]() |
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PDB format | ![]() | 81.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.5 KB | Display | ![]() |
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Full document | ![]() | 496.2 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g4eSC ![]() 1g4pC ![]() 1g4sC ![]() 1g4tC ![]() 1g67C ![]() 1g6cC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24434.789 Da / Num. of mol.: 2 / Mutation: S130A Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH 2-METHYL-5-METHYLENE-5H-PYRIMIDIN-4-YLIDENEAMINE, 4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE AND PYROPHOSPHATE Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 287 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ICP.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/TZP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ICP.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/TZP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: hanging drop vapor diffusion with micro seeding / pH: 7.5 Details: 75mM TRIS-HCl, 75 mM MgCl2, 21-22% PEG4000, pH 7.5, hanging drop vapor diffusion with micro seeding, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / Details: Chiu, H.-J., (1999) Biochemistry, 38, 6460. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Jul 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.5→42.86 Å / Num. obs: 61893 / % possible obs: 92.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 7.4 |
Reflection | *PLUS Num. obs: 63282 / % possible obs: 94.2 % |
Reflection shell | *PLUS % possible obs: 69.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G4E Resolution: 1.5→19.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2362308.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Maximum Likelihood Function
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.98 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.228 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.259 / % reflection Rfree: 5 % / Rfactor Rwork: 0.251 |