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Yorodumi- PDB-6upe: Structure of trehalose-6-phosphate phosphatase from Salmonella ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6upe | ||||||
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Title | Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium inhibited by 4-n-octylphenyl alpha-D-glucopyranoside-6-sulfate | ||||||
Components | Trehalose-phosphate phosphatase | ||||||
Keywords | HYDROLASE / HAD Superfamily / Rossmann fold / sugar binding | ||||||
Function / homology | Function and homology information trehalose-phosphatase / trehalose-phosphatase activity / trehalose biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.244 Å | ||||||
Authors | Harvey, C.M. / O'Toole, K.H. / Allen, K.N. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2020 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6upe.cif.gz | 115.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6upe.ent.gz | 85.7 KB | Display | PDB format |
PDBx/mmJSON format | 6upe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/6upe ftp://data.pdbj.org/pub/pdb/validation_reports/up/6upe | HTTPS FTP |
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-Related structure data
Related structure data | 6upbSC 6upcC 6updC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Salmonella typhimurium (strain SL1344) (bacteria) Strain: SL1344 / Gene: otsB, SL1344_1863 / Plasmid: pET15bTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E1WGG9, trehalose-phosphatase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % / Description: rod |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 400 mM lithium citrate, 30 mM magnesium chloride, 40 mM mixture of MES, MOPS, and TAPS at pH 7.5), and 0.5 uL ...Details: Drop contained: 1.5 uL 40 mg/mL protein, 2 uL reservoir solution (15% PEG 3350, 400 mM lithium citrate, 30 mM magnesium chloride, 40 mM mixture of MES, MOPS, and TAPS at pH 7.5), and 0.5 uL 1:10^3 dilution of seed stock prepared according to Seed Bead protocol. Crystals were transferred to drop containing 18% PEG 3350, 400mM lithium citrate, 40 mM magnesium chloride, 10% ethylene glycol, and 1mM OGS for 24 prior to cryocooling |
-Data collection
Diffraction | Mean temperature: 290 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.378 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 23, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.378 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.24→50 Å / Num. obs: 24547 / % possible obs: 99.3 % / Redundancy: 4 % / Biso Wilson estimate: 37.51 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.06 / Rrim(I) all: 0.123 / Χ2: 2.645 / Net I/σ(I): 9.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UPB Resolution: 2.244→37.402 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.29 / 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: 101.68 Å2 / Biso mean: 43.978 Å2 / Biso min: 20.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.244→37.402 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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