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Yorodumi- PDB-7p1f: Structure of KDNase from Aspergillus terrerus in complex with 2,3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p1f | |||||||||
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Title | Structure of KDNase from Aspergillus terrerus in complex with 2,3-didehydro-2,3-dideoxy-D-glycero-D-galacto-nonulosonic acid. | |||||||||
Components | Sialidase domain-containing protein | |||||||||
Keywords | CARBOHYDRATE / Carbohydrate Metabolism / Enzyme Structure / Protein Structure / KDN / KDNase / Sialic Acid / Sialidase | |||||||||
Function / homology | BNR repeat-like domain / exo-alpha-sialidase activity / Sialidase family / Sialidase / Sialidase superfamily / metal ion binding / Chem-KFN / Sialidase domain-containing protein Function and homology information | |||||||||
Biological species | Aspergillus terreus (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | |||||||||
Authors | Gloster, T.M. / McMahon, S.A. | |||||||||
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 | 7p1f.cif.gz | 350.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p1f.ent.gz | 280.2 KB | Display | PDB format |
PDBx/mmJSON format | 7p1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p1f_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7p1f_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7p1f_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 7p1f_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/7p1f ftp://data.pdbj.org/pub/pdb/validation_reports/p1/7p1f | HTTPS FTP |
-Related structure data
Related structure data | 7p1bC 7p1dC 7p1eC 7p1oC 7p1qC 7p1rC 7p1sC 7p1uC 7p1vC 2xzkS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 44602.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus terreus (strain NIH 2624 / FGSC A1156) (mold) Strain: NIH 2624 / FGSC A1156 / Gene: ATEG_04964 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0CMX0 #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Chemical | #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: 2.27 Å3/Da / Density % sol: 45.82 % |
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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: 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: 1.29→92.8 Å / Num. obs: 129965 / % possible obs: 96.3 % / Redundancy: 2.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.29→1.31 Å / Rmerge(I) obs: 0.68 / Num. unique obs: 8132 / CC1/2: 0.479 / % possible all: 86.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xzk Resolution: 1.45→92.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.148 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.07 / 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: 723.02 Å2 / Biso mean: 17.116 Å2 / Biso min: 5.41 Å2
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Refinement step | Cycle: final / Resolution: 1.45→92.8 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: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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