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- PDB-2wt1: Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wt1 | |||||||||
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Title | Galectin domain of porcine adenovirus type 4 NADC-1 isolate fibre complexed with lacto-N-neo-tetraose | |||||||||
![]() | PUTATIVE FIBER PROTEIN | |||||||||
![]() | VIRAL PROTEIN | |||||||||
Function / homology | ![]() galactoside binding / viral capsid / carbohydrate binding / cell adhesion / membrane raft / virion attachment to host cell / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Guardado-Calvo, P. / Munoz, E.M. / Llamas-Saiz, A.L. / Fox, G.C. / Glasgow, J.N. / van Raaij, M.J. | |||||||||
![]() | ![]() Title: Crystallographic structure of porcine adenovirus type 4 fiber head and galectin domains. Authors: Guardado-Calvo, P. / Munoz, E.M. / Llamas-Saiz, A.L. / Fox, G.C. / Kahn, R. / Curiel, D.T. / Glasgow, J.N. / van Raaij, M.J. #1: Journal: Virus Res. / Year: 1995 Title: Sequence Analysis of the Fiber Genomic Region of a Porcine Adenovirus Predicts a Novel Fiber Protein. Authors: Kleiboeker, S.B. #2: Journal: Cancer Biol.Ther. / Year: 2008 Title: Characterization of Infectivity of Knob-Modified Adenoviral Vectors in Glioma. Authors: Paul, C.P.L. / Everts, M. / Glasgow, J.N. / Dent, P. / Fisher, P.B. / Ulasov, I.V. / Lesniak, M.S. / Stoff-Khalili, M.A. / Roth, J.C. / Preuss, M.A. / Dirven, C.M.F. / Lamfers, M.L.M. / ...Authors: Paul, C.P.L. / Everts, M. / Glasgow, J.N. / Dent, P. / Fisher, P.B. / Ulasov, I.V. / Lesniak, M.S. / Stoff-Khalili, M.A. / Roth, J.C. / Preuss, M.A. / Dirven, C.M.F. / Lamfers, M.L.M. / Siegal, G.P. / Zhu, Z.B. / Curiel, D.T. #3: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. Year: 2009 Title: Crystallization of the head and galectin-like domains of porcine adenovirus isolate NADC-1 fibre. Authors: Guardado-Calvo, P. / Llamas-Saiz, A.L. / Fox, G.C. / Glasgow, J.N. / van Raaij, M.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 144.9 KB | Display | ![]() |
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PDB format | ![]() | 111.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 736.4 KB | Display | ![]() |
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Full document | ![]() | 739 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 20.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wstC ![]() 2wsuSC ![]() 2wsvC ![]() 2wt0C ![]() 2wt2C C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 37909.156 Da / Num. of mol.: 1 / Fragment: GALECTIN DOMAIN, RESIDUES 393-703 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | BETA-D-GALACTOSE (GAL): PART OF OLIGOMER ALPHA-D-GLUCOSE (BGC): PART OF OLIGOMER N-ACETYL-D- ...BETA-D-GALACTOSE (GAL): PART OF OLIGOMER ALPHA-D-GLUCOSE (BGC): PART OF OLIGOMER N-ACETYL-D-GLUCOSAMIN | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | pH: 8 Details: 10 MM TRIS-HCL PH 8.0, 27% (W/V) POLY -ETHYLENE GLYCOL 3350, 200 MM LITHIUM NITRATE 5 MM DITHIOTHREITOL, 5 MM LACTO-N-NEO-TETRAOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 26, 2009 Details: TWO CYLINDRICAL VERTICAL FOCUSING PARABOLIC MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI (111), SI(311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 23751 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 91.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WSU CHAIN A Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.434 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 32.697 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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