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Yorodumi- PDB-6upc: Structure of trehalose-6-phosphate phosphatase from Salmonella ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6upc | ||||||
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Title | Structure of trehalose-6-phosphate phosphatase from Salmonella typhimurium in complex with trehalose 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 / Resolution: 2.505 Å | ||||||
Authors | O'Toole, K.H. / Harvey, C.M. / 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 | 6upc.cif.gz | 113 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6upc.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 6upc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6upc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6upc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6upc_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6upc_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/6upc ftp://data.pdbj.org/pub/pdb/validation_reports/up/6upc | HTTPS FTP |
-Related structure data
Related structure data | 6upbSC 6updC 6upeC 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 246 / Label seq-ID: 1 - 246
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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: 49.16 % / 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 (19% PEG 3350, 375 mM lithium citrate, 10 mM magnesium chloride 2% 1,4 dioxane) and 0.5 uL 1:10^9 dilution of seed stock ...Details: Drop Contained: 2 uL 40 mg/mL protein, 2 uL reservoir solution (19% PEG 3350, 375 mM lithium citrate, 10 mM magnesium chloride 2% 1,4 dioxane) and 0.5 uL 1:10^9 dilution of seed stock prepared according to the Seed Bead protocol. Crystals were transferred to a drop containing 24% PEG 3350, 50 mM lithium citrate, 100 mM magnesium chloride, 10% ethylene glycol and 5 mM trehalose 6-phosphate for 1 hours prior to cryocooling |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9201 Å / Relative weight: 1 |
Reflection | Resolution: 2.505→29.273 Å / Num. obs: 17698 / % possible obs: 99.2 % / Redundancy: 2 % / Biso Wilson estimate: 41.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.03 |
Reflection shell | Resolution: 2.505→2.595 Å / Rmerge(I) obs: 0.4797 / Num. unique obs: 1678 / CC1/2: 0.616 / % possible all: 94.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UPB Resolution: 2.505→29.273 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.89 Å2 / Biso mean: 51.4037 Å2 / Biso min: 16.18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.505→29.273 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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