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- PDB-3c8u: Crystal structure of putative fructose transport system kinase (Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c8u | ||||||
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Title | Crystal structure of putative fructose transport system kinase (YP_612366.1) from Silicibacter sp. TM1040 at 1.95 A resolution | ||||||
![]() | Fructokinase | ||||||
![]() | TRANSFERASE / YP_612366.1 / putative fructose transport system kinase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | fructokinase / fructokinase activity / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Fructokinase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of putative fructose transport system kinase (YP_612366.1) from Silicibacter sp. TM1040 at 1.95 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58 KB | Display | ![]() |
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PDB format | ![]() | 44.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 414.4 KB | Display | ![]() |
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Full document | ![]() | 416.4 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 19.1 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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Components on special symmetry positions |
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Components
#1: Protein | Mass: 22728.459 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: NANODROP, 23.1% PEG 3350, 0.214M Sodium fluoride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 13, 2008 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→35.267 Å / Num. obs: 15859 / % possible obs: 91.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.87 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.95 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. THE REFLECTIONS WITHIN RESOLUTION RANGES 3.70-3.64 AND 2.3-2.2 ANGSTROM WERE EXCLUDED DURING INTEGRATION AND SUBSEQUENT STEPS DUE TO THE PRESENCE OF ICE RINGS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.647 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→35.267 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 22.5935 Å / Origin y: 12.4151 Å / Origin z: 38.2847 Å
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