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Open data
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Basic information
| Entry | Database: PDB / ID: 9eu3 | |||||||||
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| Title | GH29A alpha-L-fucosidase | |||||||||
Components | Alpha-L-fucosidase | |||||||||
Keywords | HYDROLASE / GH29A / GH29 / fucosidase / fucose | |||||||||
| Function / homology | Function and homology informationalpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process / lysosome / metal ion binding Similarity search - Function | |||||||||
| Biological species | Tannerella forsythia (bacteria) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | |||||||||
Authors | Yang, Y.Y. / Zeuner, B. / Morth, J.P. | |||||||||
| Funding support | Denmark, 2items
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Citation | Journal: Febs J. / Year: 2025Title: Structural elucidation and characterization of GH29A alpha-l-fucosidases and the effect of pH on their transglycosylation. Authors: Yang, Y. / Holck, J. / Thorhallsson, A.T. / Hunt, C.J. / Yang, H. / Morth, J.P. / Meyer, A.S. / Zeuner, B. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9eu3.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9eu3.ent.gz | 836.8 KB | Display | PDB format |
| PDBx/mmJSON format | 9eu3.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9eu3_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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| Full document | 9eu3_full_validation.pdf.gz | 1.8 MB | Display | |
| Data in XML | 9eu3_validation.xml.gz | 76.5 KB | Display | |
| Data in CIF | 9eu3_validation.cif.gz | 98.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/9eu3 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/9eu3 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9eu1C ![]() 9eu2C ![]() 9eu4C C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Assembly
| Deposited unit | ![]()
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| Components on special symmetry positions |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
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Movie
Controller
Components
About Yorodumi




Tannerella forsythia (bacteria)
X-RAY DIFFRACTION
Denmark, 2items
Citation




PDBj




