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Yorodumi- PDB-5ofu: Crystal structure of Leishmania major fructose-1,6-bisphosphatase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ofu | ||||||
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Title | Crystal structure of Leishmania major fructose-1,6-bisphosphatase in T-state. | ||||||
Components | FBP protein | ||||||
Keywords | TRANSFERASE / Allostery / Gluconeogenesis | ||||||
Function / homology | Function and homology information sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / glycosome / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / nucleotide binding / metal ion binding ...sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / glycosome / fructose 6-phosphate metabolic process / fructose metabolic process / fructose 1,6-bisphosphate metabolic process / gluconeogenesis / nucleotide binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Yuan, M. / Vasquez-Valdivieso, M.G. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition. Authors: Yuan, M. / Vasquez-Valdivieso, M.G. / McNae, I.W. / Michels, P.A.M. / Fothergill-Gilmore, L.A. / Walkinshaw, M.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ofu.cif.gz | 502 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ofu.ent.gz | 417.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ofu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/5ofu ftp://data.pdbj.org/pub/pdb/validation_reports/of/5ofu | HTTPS FTP |
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-Related structure data
Related structure data | 5oeyC 5oezC 5fbpS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 38872.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: FBP, LMJF_04_1160 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O97193, fructose-bisphosphatase #2: Chemical | ChemComp-AMP / #3: Sugar | ChemComp-F6P / #4: Chemical | #5: 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: 2.24 Å3/Da / Density % sol: 44.99 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 19% w/v PEG 3,350, 5% glycerol, 79% well buffer (0.05 M citric acid, 0.05 M Bis-Tris propane) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→70.25 Å / Num. obs: 42513 / % possible obs: 99.9 % / Redundancy: 5.5 % / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.62→2.714 Å / Rmerge(I) obs: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FBP Resolution: 2.62→70.25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 25.146 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R Free: 0.291 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.203 Å2
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Refinement step | Cycle: 1 / Resolution: 2.62→70.25 Å
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Refine LS restraints |
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