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Open data
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Basic information
Entry | Database: PDB / ID: 8pe1 | ||||||
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Title | Crystal structure of Gel4 in complex with Nanobody 4 | ||||||
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![]() | TRANSFERASE / Transglycosylase / b-1 / 3-glucan / nanobodies / fungal diseases | ||||||
Function / homology | ![]() 1,3-beta-glucanosyltransferase activity / fungal-type cell wall (1->3)-beta-D-glucan biosynthetic process / fungal-type cell wall organization / Transferases; Glycosyltransferases; Hexosyltransferases / side of membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Macias-Leon, J. / Redrado-Hernandez, S. / Castro-Lopez, J. / Sanz, A.B. / Arias, M. / Farkas, V. / Vincke, C. / Muyldermans, S. / Pardo, J. / Arroyo, J. ...Macias-Leon, J. / Redrado-Hernandez, S. / Castro-Lopez, J. / Sanz, A.B. / Arias, M. / Farkas, V. / Vincke, C. / Muyldermans, S. / Pardo, J. / Arroyo, J. / Galvez, E. / Hurtado-Guerrero, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Broad protection against invasive fungal disease from a nanobody targeting the active site of fungal b-1,3-glucanosyltransferases. Authors: Redrado-Hernandez, S. / Macias-Leon, J. / Castro-Lopez, J. / Sanz, A.B. / Dolader, E. / Arias, M. / Gonzalez-Ramirez, A.M. / Sanchez-Navarro, D. / Petryk, Y. / Farkas, V. / Vincke, C. / ...Authors: Redrado-Hernandez, S. / Macias-Leon, J. / Castro-Lopez, J. / Sanz, A.B. / Dolader, E. / Arias, M. / Gonzalez-Ramirez, A.M. / Sanchez-Navarro, D. / Petryk, Y. / Farkas, V. / Vincke, C. / Muyldermans, S. / Garcia-Barbazan, I. / Del Agua, C. / Zaragoza, O. / Arroyo, J. / Pardo, J. / Galvez, E. / Hurtado-Guerrero, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.3 KB | Display | ![]() |
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PDB format | ![]() | 202 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 510 KB | Display | ![]() |
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Full document | ![]() | 534.3 KB | Display | |
Data in XML | ![]() | 51.3 KB | Display | |
Data in CIF | ![]() | 73.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8pe2C ![]() 2w62S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 50267.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 13775.122 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / #4: Sugar | ChemComp-MAN / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.3 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Halogens, buffer system 3, P500MME P20K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20.01 Å / Num. obs: 104001 / % possible obs: 99.6 % / Redundancy: 5.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.182 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.9→2 Å / Rmerge(I) obs: 1.588 / Mean I/σ(I) obs: 1 / Num. unique obs: 15033 / CC1/2: 0.537 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2W62 Resolution: 1.9→20.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.214 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 29.531 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→20.01 Å
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Refine LS restraints |
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