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- PDB-3ceu: Crystal structure of thiamine phosphate pyrophosphorylase (BT_064... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ceu | ||||||
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Title | Crystal structure of thiamine phosphate pyrophosphorylase (BT_0647) from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR268 | ||||||
![]() | Thiamine phosphate pyrophosphorylase | ||||||
![]() | TRANSFERASE / TIM barrel-like protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | ![]() thiamine-phosphate diphosphorylase activity / thiamine biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Foote, E.L. / Maglaqui, M. / Ciccosanti, C. / Zhao, L. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Foote, E.L. / Maglaqui, M. / Ciccosanti, C. / Zhao, L. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of thiamine phosphate pyrophosphorylase (BT_0647) from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR268. Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Janjua, H. / Mao, L. / Xiao, R. / Foote, E.L. / Maglaqui, M. / Ciccosanti, C. / Zhao, L. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.9 KB | Display | ![]() |
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PDB format | ![]() | 74 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24760.535 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Bacteroides thetaiotaomicron / Strain: VPI-5482 / DSM 2079 / NCTC 10582 / Gene: BT_0647 / Plasmid: pET21 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.78 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM MES pH 6.0, 20% PEG 8000, 100 mM Magnesium nitrate, MICROBATCH UNDER OIL, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2008 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97902 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 34307 / Num. obs: 34307 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.05 / Net I/σ(I): 13.95 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.96 / Num. unique all: 3462 / Rsym value: 0.196 / % possible all: 96.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.5053 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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