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Open data
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Basic information
Entry | Database: PDB / ID: 7p1b | |||||||||
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Title | Apo structure of KDNase from Aspergillus Terrerus | |||||||||
![]() | Sialidase domain-containing protein | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | BNR repeat-like domain / ![]() ![]() ![]() ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gloster, T.M. / McMahon, S.A. | |||||||||
Funding support | 1items
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![]() | ![]() 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 | ![]() | 97 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7p1dC ![]() 7p1eC ![]() 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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1 |
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Unit cell |
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Components
#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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#2: Water | ChemComp-HOH / ![]() |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.19 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / 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 / Detector: PIXEL / Date: Dec 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.45→40.81 Å / Num. obs: 69104 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.99 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.45→1.49 Å / Num. unique obs: 5046 / CC1/2: 0.68 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2xcy Resolution: 1.45→40.81 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.739 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.085 / 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: 73.41 Å2 / Biso mean: 27.933 Å2 / Biso min: 13.73 Å2
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Refinement step | Cycle: final / Resolution: 1.45→40.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.486 Å / Rfactor Rfree error: 0
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