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Yorodumi- PDB-7p1r: Structure of Trichophyton Rubrum KDNase in complex with 2,3-diflu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p1r | ||||||
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Title | Structure of Trichophyton Rubrum KDNase in complex with 2,3-difluoro-KDN | ||||||
Components | Extracellular sialidase/neuraminidase | ||||||
Keywords | CARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase / Trichophyton rubrum | ||||||
Function / homology | Function and homology information exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Trichophyton rubrum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Gloster, T.M. / McMahon, S.A. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2021 Title: Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens. Authors: Nejatie, A. / Steves, E. / Gauthier, N. / Baker, J. / Nesbitt, J. / McMahon, S.A. / Oehler, V. / Thornton, N.J. / Noyovitz, B. / Khazaei, K. / Byers, B.W. / Zandberg, W.F. / Gloster, T.M. / ...Authors: Nejatie, A. / Steves, E. / Gauthier, N. / Baker, J. / Nesbitt, J. / McMahon, S.A. / Oehler, V. / Thornton, N.J. / Noyovitz, B. / Khazaei, K. / Byers, B.W. / Zandberg, W.F. / Gloster, T.M. / Moore, M.M. / Bennet, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p1r.cif.gz | 347.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p1r.ent.gz | 277.4 KB | Display | PDB format |
PDBx/mmJSON format | 7p1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p1r_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7p1r_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7p1r_validation.xml.gz | 73.2 KB | Display | |
Data in CIF | 7p1r_validation.cif.gz | 112.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/7p1r ftp://data.pdbj.org/pub/pdb/validation_reports/p1/7p1r | HTTPS FTP |
-Related structure data
Related structure data | 7p1bC 7p1dC 7p1eC 7p1fC 7p1oC 7p1qC 7p1sC 7p1uC 7p1vC 2xcyS 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:
NCS ensembles :
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-Components
#1: Protein | Mass: 42214.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichophyton rubrum (fungus) / Gene: A7C99_5399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A178EUH2 #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-NA / #4: Sugar | ChemComp-FKD / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 25% PEG 1500, 0.1M SPG pH4 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→95.2 Å / Num. obs: 158507 / % possible obs: 96.6 % / Redundancy: 2.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 7614 / CC1/2: 0.712 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XCY Resolution: 1.75→95.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.774 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.76 Å2 / Biso mean: 23.655 Å2 / Biso min: 10.72 Å2
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Refinement step | Cycle: final / Resolution: 1.75→95.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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