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- PDB-7p1u: Structure of KDNase from Trichophyton Rubrum in complex with 2-ke... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p1u | ||||||
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Title | Structure of KDNase from Trichophyton Rubrum in complex with 2-keto-3-deoxynononic acid | ||||||
![]() | Extracellular sialidase/neuraminidase | ||||||
![]() | CARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase | ||||||
Function / homology | ![]() exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / intracellular membrane-bounded organelle / membrane / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloster, T.M. / McMahon, S.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347 KB | Display | ![]() |
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PDB format | ![]() | 280 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 58.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p1bC ![]() 7p1dC ![]() 7p1eC ![]() 7p1fC ![]() 7p1oC ![]() 7p1qC ![]() 7p1rC ![]() 7p1sC ![]() 7p1vC ![]() 2xcyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
#1: Protein | Mass: 42214.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% Peg 3350, 0.2m K formate |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91188 Å / Relative weight: 1 |
Reflection | Resolution: 0.99→47.73 Å / Num. obs: 405311 / % possible obs: 98.5 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 0.99→1.01 Å / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1 / Num. unique obs: 18293 / CC1/2: 0.7 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2xcy Resolution: 0.99→47.73 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.158 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / 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: 192.06 Å2 / Biso mean: 12.478 Å2 / Biso min: 5.14 Å2
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Refinement step | Cycle: final / Resolution: 0.99→47.73 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 14069 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05
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LS refinement shell | Resolution: 0.99→1.016 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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