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- PDB-7p1e: Structure of KDNase from Aspergillus Terrerus in complex with 2,3... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p1e | |||||||||
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Title | Structure of KDNase from Aspergillus Terrerus in complex with 2,3-difluoro-2-keto-3-deoxynononic acid | |||||||||
![]() | Sialidase domain-containing protein | |||||||||
![]() | 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 | ![]() | 100.9 KB | Display | ![]() |
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PDB format | ![]() | 72.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p1bC ![]() 7p1dC ![]() 7p1fC ![]() 7p1oC ![]() 7p1qC ![]() 7p1rC ![]() 7p1sC ![]() 7p1uC ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 44602.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: NIH 2624 / FGSC A1156 / Gene: ATEG_04964 / Production host: ![]() ![]() |
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-Sugars , 2 types, 2 molecules ![](data/chem/img/FKD.gif)
![](data/chem/img/K99.gif)
![](data/chem/img/K99.gif)
#2: Sugar | ChemComp-FKD / |
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#3: Sugar | ChemComp-K99 / ( |
-Non-polymers , 4 types, 357 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-CA / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG 6K, 0.1M MES pH6 , 0.2M Calcium Chloride |
-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 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: 1.53→61.35 Å / Num. obs: 58094 / % possible obs: 99.8 % / Redundancy: 2.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.53→1.57 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.272 / Mean I/σ(I) obs: 1 / Num. unique obs: 4263 / CC1/2: 0.53 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2xcy Resolution: 1.53→61.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.09 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.084 / 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: 85.89 Å2 / Biso mean: 19.55 Å2 / Biso min: 10.6 Å2
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Refinement step | Cycle: final / Resolution: 1.53→61.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.566 Å / Rfactor Rfree error: 0
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