+Open data
-Basic information
Entry | Database: PDB / ID: 2nzx | ||||||
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Title | Crystal Structure of alpha1,3-Fucosyltransferase with GDP | ||||||
Components | Alpha1,3-fucosyltransferase | ||||||
Keywords | TRANSFERASE / Alpha1 / 3-Fucosyltransferase / Fucosyltransferase / FucT / GT 10 | ||||||
Function / homology | Function and homology information 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase / 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase activity / fucosylation / fucose binding / lipopolysaccharide biosynthetic process / protein glycosylation / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Sun, H.Y. / Ko, T.P. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2007 Title: Structure and mechanism of Helicobacter pylori fucosyltransferase. A basis for lipopolysaccharide variation and inhibitor design. Authors: Sun, H.Y. / Lin, S.W. / Ko, T.P. / Pan, J.F. / Liu, C.L. / Lin, C.N. / Wang, A.H. / Lin, C.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nzx.cif.gz | 278.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nzx.ent.gz | 219.6 KB | Display | PDB format |
PDBx/mmJSON format | 2nzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nzx ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nzx | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43123.359 Da / Num. of mol.: 3 / Fragment: C-termincal truncated domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: NCTC 11639 / Gene: AF008596 / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O30511, 4-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase #2: Chemical | #3: Chemical | ChemComp-SO4 / | #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: 2.6 Å3/Da / Density % sol: 52.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 4-5% PEG 3350, 0.2-0.4M ammonium phosphate, 0.1M Bis-Tris , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 108428 / Num. obs: 104965 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 42.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.4 / Num. unique all: 10752 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.02
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