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Yorodumi- PDB-4xqa: CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xqa | |||||||||||||||||||||
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Title | CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0462 | |||||||||||||||||||||
Components | Fiber | |||||||||||||||||||||
Keywords | VIRAL PROTEIN / ADENOVIRUS / FIBER KNOB / PROTEIN CARBOHYDRATE INTERACTION / SIALIC ACID / CARBOHYDRATE MIMIC / MULTIVALENT LIGAND | |||||||||||||||||||||
Function / homology | Function and homology information adhesion receptor-mediated virion attachment to host cell / viral capsid / cell adhesion / symbiont entry into host cell / host cell nucleus / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | Human adenovirus 37 | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4072 Å | |||||||||||||||||||||
Authors | Stehle, T. / Liaci, A.M. | |||||||||||||||||||||
Funding support | Germany, Sweden, 6items
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Citation | Journal: Org.Biomol.Chem. / Year: 2015 Title: Triazole linker-based trivalent sialic acid inhibitors of adenovirus type 37 infection of human corneal epithelial cells. Authors: Caraballo, R. / Saleeb, M. / Bauer, J. / Liaci, A.M. / Chandra, N. / Storm, R.J. / Frangsmyr, L. / Qian, W. / Stehle, T. / Arnberg, N. / Elofsson, M. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xqa.cif.gz | 262.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xqa.ent.gz | 209.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xqa_validation.pdf.gz | 948.8 KB | Display | wwPDB validaton report |
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Full document | 4xqa_full_validation.pdf.gz | 957.6 KB | Display | |
Data in XML | 4xqa_validation.xml.gz | 29 KB | Display | |
Data in CIF | 4xqa_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/4xqa ftp://data.pdbj.org/pub/pdb/validation_reports/xq/4xqa | HTTPS FTP |
-Related structure data
Related structure data | 4k6tC 4k6uC 4k6vC 4k6wC 4xqbC 1uxeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21716.535 Da / Num. of mol.: 3 / Fragment: UNP residues 177-365 Source method: isolated from a genetically manipulated source Details: FRAGMENT: FIBER KNOB / Source: (gene. exp.) Human adenovirus 37 / Gene: L5 / Plasmid: PPROEX HTB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64823 #2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-423 / ( | #5: Water | ChemComp-HOH / | |
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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: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 26% PEG 8000, 0.1M HEPES, 0.05M zinc acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014 |
Radiation | Monochromator: Fixed-exit LN2 cooled Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4072→50 Å / Num. obs: 131319 / % possible obs: 99.6 % / Redundancy: 12.75 % / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.4072→1.49 Å / Redundancy: 12.63 % / Rmerge(I) obs: 1.545 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.844 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1uxe Resolution: 1.4072→47.272 Å / FOM work R set: 0.8955 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.43 Å2 / Biso mean: 33.16 Å2 / Biso min: 18.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4072→47.272 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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