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- PDB-4m4v: Structural evaluation R171L mutant of the aspergillus fumigatus k... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4m4v | ||||||
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Title | Structural evaluation R171L mutant of the aspergillus fumigatus kdnase (sialidase) | ||||||
![]() | Extracellular sialidase/neuraminidase, putative | ||||||
![]() | HYDROLASE / KDNase | ||||||
Function / homology | ![]() exo-alpha-sialidase activity / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / intracellular membrane-bounded organelle / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Telford, J.C. / Taylor, G.L. | ||||||
![]() | ![]() Title: Active site mutants of a fungal KDNase Authors: Yeung, J.Y. / Telford, J.C. / S Shidmoossavee, F. / Bennet, A.J. / Taylor, G.L. / Moore, M.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 192.2 KB | Display | ![]() |
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PDB format | ![]() | 148.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 847.5 KB | Display | ![]() |
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Full document | ![]() | 851.1 KB | Display | |
Data in XML | ![]() | 41.1 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4m4nC ![]() 4m4uC ![]() 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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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/DAN.gif)
![](data/chem/img/DAN.gif)
#1: Protein | Mass: 46232.559 Da / Num. of mol.: 2 / Mutation: R171L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | ChemComp-DAN / | |
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-Non-polymers , 4 types, 1196 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-NO3 / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% (w/v) PEG 3350, 0.2M sodium nitrate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 27, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.836→12.394 Å / Num. all: 70446 / Num. obs: 70446 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.086 / Net I/σ(I): 13.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 2XCY Resolution: 1.84→12.39 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.293 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.119 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.48 Å2 / Biso mean: 12.0909 Å2 / Biso min: 2.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.84→12.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.836→1.883 Å / Total num. of bins used: 20
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