+Open data
-Basic information
Entry | Database: PDB / ID: 9fym | ||||||
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Title | Lacto-N-biosidase from Treponema denticola ATCC 35405 | ||||||
Components | Glycoside hydrolase family 20 catalytic domain-containing protein | ||||||
Keywords | HYDROLASE / lacto-N-biosidase / GH20 | ||||||
Function / homology | Hexosaminidase D-like / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / beta-N-acetylhexosaminidase activity / : / Glycoside hydrolase superfamily / carbohydrate metabolic process / IMIDAZOLE / Glycoside hydrolase family 20 catalytic domain-containing protein Function and homology information | ||||||
Biological species | Treponema denticola ATCC 35405 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Vuillemin, M. / Siebenhaar, S. / Zeuner, B. / Morth, J.P. | ||||||
Funding support | Denmark, 1items
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Citation | Journal: Chembiochem / Year: 2024 Title: Discovery of Lacto-N-biosidases and a Novel N-Acetyllactosaminidase Activity in the CAZy Family GH20: Functional Diversity and Structural Insights. Authors: Vuillemin, M. / Muschiol, J. / Zhang, Y. / Holck, J. / Barrett, K. / Morth, J.P. / Meyer, A.S. / Zeuner, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9fym.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9fym.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 9fym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fym_validation.pdf.gz | 440.6 KB | Display | wwPDB validaton report |
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Full document | 9fym_full_validation.pdf.gz | 443.2 KB | Display | |
Data in XML | 9fym_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 9fym_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/9fym ftp://data.pdbj.org/pub/pdb/validation_reports/fy/9fym | HTTPS FTP |
-Related structure data
Related structure data | 9fylC 9fynC 9fyoC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37816.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Signal peptide has been removed, additional GS (from Thrombin cleavage). Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria) Gene: TDE_1723 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73LY9 | ||||||||
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#2: Chemical | ChemComp-IMD / | ||||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.76 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% w/v PEG 8000, 9% ethylene glycol, 0.1M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→48.15 Å / Num. obs: 77556 / % possible obs: 99.58 % / Redundancy: 8.2 % / Biso Wilson estimate: 17.71 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08324 / Rpim(I) all: 0.03112 / Rrim(I) all: 0.08909 / Net I/σ(I): 11.31 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 7469 / CC1/2: 0.464 / Rpim(I) all: 1 / Rrim(I) all: 1 / % possible all: 97.97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.34→48.15 Å / SU ML: 0.175 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4484 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→48.15 Å
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Refine LS restraints |
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LS refinement shell |
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