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Open data
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Basic information
Entry | Database: PDB / ID: 2wst | ||||||
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Title | Head domain of porcine adenovirus type 4 NADC-1 isolate fibre | ||||||
![]() | PUTATIVE FIBER PROTEIN![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() 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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Download
PDBx/mmCIF format | ![]() | 411.8 KB | Display | ![]() |
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PDB format | ![]() | 342.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wsuC ![]() 2wsvC ![]() 2wt0C ![]() 2wt1C ![]() 2wt2C ![]() 1knbS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 2 / Auth seq-ID: 116 - 291 / Label seq-ID: 33 - 208
NCS oper:
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Components
#1: Protein | ![]() Mass: 22289.850 Da / Num. of mol.: 6 / Fragment: HEAD DOMAIN, RESIDUES 116-291 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.9 Å3/Da / Density % sol: 79.3 % / Description: NONE |
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Crystal grow![]() | pH: 8 Details: 10 MM TRIS-HCL PH 8.0, 1 MM EDTA, 1-10% (W/V) POLY-ETHYLENE GLYCOL 8000, 1 M LITHIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS KAPPACCD 2000 / Detector: CCD / Date: Jul 2, 2008 / Details: CONFOCAL MULTILAYER GRADED MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.2→40 Å / Num. obs: 45035 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 62.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 3.2→3.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.9 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KNB Resolution: 3.2→29.21 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 29.974 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
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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: 54.59 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→29.21 Å
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Refine LS restraints |
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