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- PDB-3cwi: Crystal structure of thiamine biosynthesis protein (ThiS) from Ge... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cwi | ||||||
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Title | Crystal structure of thiamine biosynthesis protein (ThiS) from Geobacter metallireducens. Northeast Structural Genomics Consortium Target GmR137 | ||||||
![]() | Thiamine-biosynthesis protein ThiS | ||||||
![]() | BIOSYNTHETIC PROTEIN / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | ![]() ThiS, thiamine-biosynthesis / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Foote, E.L. / Wang, H. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of thiamine biosynthesis protein (ThiS) from Geobacter metallireducens. Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Maglaqui, M. / Ciccosanti, C. / Foote, E.L. / Wang, H. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.1 KB | Display | ![]() |
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PDB format | ![]() | 16.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.7 KB | Display | ![]() |
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Full document | ![]() | 422.4 KB | Display | |
Data in XML | ![]() | 5.2 KB | Display | |
Data in CIF | ![]() | 6.5 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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Unit cell |
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Details | AUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE |
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Components
#1: Protein | Mass: 8624.253 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Geobacter metallireducens / Strain: GS-15 / DSM 7210 / Gene: ThiS, Gmet_1567 / Plasmid: pET21 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.52 % Description: The structure factor file contains Friedel pairs |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM NaCl, 5 mM DTT. Reservoir solution: 100 mM Sodium acetate pH 5.0, 18% PEG 8000, 200 mM Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 2, 2008 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 11436 / Num. obs: 11436 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.5 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.063 / Net I/σ(I): 40.74 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.54 / Num. unique all: 1152 / Rsym value: 0.328 / % possible all: 99.8 |
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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: 59.014 Å2 / ksol: 0.45 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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