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Yorodumi- PDB-6rcz: The structure of Burkholderia pseudomallei trehalose-6-phosphatase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rcz | ||||||
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Title | The structure of Burkholderia pseudomallei trehalose-6-phosphatase | ||||||
Components | Trehalose 6-phosphate phosphatase | ||||||
Keywords | HYDROLASE / phosphatase | ||||||
Function / homology | Function and homology information trehalose-phosphatase / trehalose-phosphatase activity / trehalose biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Gourlay, L.J. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Functional and structural analysis of trehalose-6-phosphate phosphatase from Burkholderia pseudomallei: Insights into the catalytic mechanism. Authors: Suthisawat, S. / Gourlay, L.J. / Bolognesi, M. / Boonyuen, U. / Vanaporn, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rcz.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rcz.ent.gz | 167.4 KB | Display | PDB format |
PDBx/mmJSON format | 6rcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/6rcz ftp://data.pdbj.org/pub/pdb/validation_reports/rc/6rcz | HTTPS FTP |
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-Related 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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-Components
#1: Protein | Mass: 28651.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria) Gene: otsB, BPSL2411 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63SB3, trehalose-phosphatase #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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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: 2.37 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: condition G1 (0.1 M Buffer System 1 (imidazole and MES monohydrate) pH 6.5, 50 % (v/v) Precipitant Mix 1 (40 % (w/v) PEG500, 20% (w/v) PEG20K)) from the Morpheus Screen (Molecular Dimensions) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→59.683 Å / Num. obs: 35129 / % possible obs: 94.6 % / Redundancy: 13 % / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.046 / Rrim(I) all: 0.161 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.74→1.946 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.1776 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1757 / CC1/2: 0.646 / Rpim(I) all: 0.538 / Rrim(I) all: 1.859 / % possible all: 69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→59.683 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→59.683 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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