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Yorodumi- PDB-3l8f: Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l8f | ||||||
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Title | Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli complexed with magnesium and phosphate | ||||||
Components | D,D-heptose 1,7-bisphosphate phosphatase | ||||||
Keywords | HYDROLASE / HAD superfamily / GMHB / D-glycero-D-manno-heptose-1 / 7-bisphosphate phosphatase / Carbohydrate metabolism / Cytoplasm / Lipopolysaccharide biosynthesis | ||||||
Function / homology | Function and homology information D,D-heptose 1,7-bisphosphate phosphatase activity / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Nguyen, H. / Peisach, E. / Allen, K.N. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) . Authors: Nguyen, H.H. / Wang, L. / Huang, H. / Peisach, E. / 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 | 3l8f.cif.gz | 48.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l8f.ent.gz | 37.6 KB | Display | PDB format |
PDBx/mmJSON format | 3l8f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l8/3l8f ftp://data.pdbj.org/pub/pdb/validation_reports/l8/3l8f | HTTPS FTP |
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-Related 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: 21268.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0200, gmhB, JW0196, yaeD / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B-834 References: UniProt: P63228, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-PO4 / |
#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: 1.97 Å3/Da / Density % sol: 37.44 % |
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 7.5 Details: 0.1M Tris, 5mM MgCl2, 25% PEG 3350, pH 7.5, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.79→50 Å / Num. obs: 29102 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Χ2: 1.004 / Net I/σ(I): 12.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 62.345 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.24 Å2 / Biso mean: 32.033 Å2 / Biso min: 3.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→50 Å
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Refine LS restraints |
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Xplor file |
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