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Yorodumi- PDB-5e0o: Brugia malayi Trehalose-6 Phosphate Phosphatase in complex with P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e0o | ||||||
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Title | Brugia malayi Trehalose-6 Phosphate Phosphatase in complex with PEG at the active site. | ||||||
Components | Trehalose-phosphatase | ||||||
Keywords | HYDROLASE / HAD / Complex / Phosphatase | ||||||
Function / homology | Function and homology information trehalose-phosphatase / carbohydrate derivative catabolic process / trehalose-phosphatase activity / trehalose biosynthetic process / dephosphorylation / magnesium ion binding Similarity search - Function | ||||||
Biological species | Brugia malayi (agent of lymphatic filariasis) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Agarwal, A. / Misra-Bhattacharya, S. / Ravishankar, R. | ||||||
Funding support | India, 1items
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Citation | Journal: To Be Published / Year: 2015 Title: Brugia malayi Trehalose Phosphate Phosphatase in complex with PEG at the active site Authors: Agarwal, A. / Misra-Bhattacharya, S. / Ravishankar, R. #1: Journal: PLoS Pathog. / Year: 2014 Title: Structure of the trehalose-6-phosphate phosphatase from Brugia malayi reveals key design principles for anthelmintic drugs. Authors: Farelli, J.D. / Galvin, B.D. / Li, Z. / Liu, C. / Aono, M. / Garland, M. / Hallett, O.E. / Causey, T.B. / Ali-Reynolds, A. / Saltzberg, D.J. / Carlow, C.K. / 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 | 5e0o.cif.gz | 184.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e0o.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 5e0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e0o_validation.pdf.gz | 456.7 KB | Display | wwPDB validaton report |
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Full document | 5e0o_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 5e0o_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 5e0o_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/5e0o ftp://data.pdbj.org/pub/pdb/validation_reports/e0/5e0o | HTTPS FTP |
-Related structure data
Related structure data | 4ofzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58740.660 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis) Gene: Bm1_08695 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A8NS89, trehalose-phosphatase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-PEG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Large good diffractable crystal grow with in 7-8 days. PH range: 6.0-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2013 |
Radiation | Monochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 3→43.859 Å / Num. obs: 18275 / % possible obs: 99.5 % / Redundancy: 25.6 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 16.25 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4OFZ Resolution: 3→43.859 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.53 / 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: 244.89 Å2 / Biso mean: 53.0636 Å2 / Biso min: 3.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→43.859 Å
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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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