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- PDB-6upd: Structure of trehalose-6-phosphate phosphatase from Salmonella ty... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6upd | ||||||
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Title | Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose | ||||||
![]() | Trehalose-phosphate phosphatase | ||||||
![]() | HYDROLASE / HAD Superfamily / Rossmann fold / sugar binding | ||||||
Function / homology | ![]() trehalose-phosphatase / trehalose-phosphatase activity / trehalose biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Harvey, C.M. / O'Toole, K.H. / Allen, K.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Analysis of Binding Determinants ofSalmonella typhimuriumTrehalose-6-phosphate Phosphatase Using Ground-State Complexes. Authors: Harvey, C.M. / O'Toole, K.H. / Liu, C. / Mariano, P. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
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PDB format | ![]() | 84.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6upbSC ![]() 6upcC ![]() 6upeC S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 29296.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: SL1344 / Gene: otsB, SL1344_1863 / Plasmid: pET15bTEV / Production host: ![]() ![]() #2: Polysaccharide | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.31 % / Description: rod |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Drop Contained: 2 uL 40 mg/mL protein, 2 uL reservoir solution (16% PEG 3350, 450 mM lithium citrate and 10 mM magnesium chloride) and 0.5 uL 1:10^3 dilution of seed stock prepared according ...Details: Drop Contained: 2 uL 40 mg/mL protein, 2 uL reservoir solution (16% PEG 3350, 450 mM lithium citrate and 10 mM magnesium chloride) and 0.5 uL 1:10^3 dilution of seed stock prepared according to the Seed Bead protocol. Crystals were transferred to a drop containing 35% PEG 3350, 166 mM lithium citrate, 166 mM magnesium chloride, 10% ethylene glycol and 50 mM trehalose for 30 minutes prior to cryocooling. |
-Data collection
Diffraction | Mean temperature: 290 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.05→106.9 Å / Num. obs: 32534 / % possible obs: 98.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 40.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.051 / Rrim(I) all: 0.098 / Net I/σ(I): 9.4 / Num. measured all: 117234 / Scaling rejects: 76 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6upb Resolution: 2.052→53.451 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.93 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.09 Å2 / Biso mean: 48.6048 Å2 / Biso min: 20.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.052→53.451 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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