+Open data
-Basic information
Entry | Database: PDB / ID: 1uxa | |||||||||
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Title | ADENOVIRUS AD37 FIBRE HEAD in complex with sialyl-lactose | |||||||||
Components | FIBER PROTEIN | |||||||||
Keywords | VIRAL PROTEIN / ADENOVIRUS / AD37 / FIBRE / RECEPTOR / SIALIC ACID / NEURAMINIC ACID / CD46 / DAF / CONJUNCTIVITIS | |||||||||
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 TYPE 37 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Burmeister, W.P. / Guilligay, D. / Cusack, S. / Wadell, G. / Arnberg, N. | |||||||||
Citation | Journal: J.Virol. / Year: 2004 Title: Crystal Structure of Species D Adenovirus Fiber Knobs and Their Sialic Acid Binding Sites Authors: Burmeister, W.P. / Guilligay, D. / Cusack, S. / Wadell, G. / Arnberg, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uxa.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxa.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 1uxa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uxa_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1uxa_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1uxa_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 1uxa_validation.cif.gz | 41.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxa ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxa | HTTPS FTP |
-Related structure data
Related structure data | 1uxbC 1uxeC 1qhvS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 21716.535 Da / Num. of mol.: 3 / Fragment: HEAD DOMAIN, RESIDUES 172-365 / Mutation: YES Source method: isolated from a genetically manipulated source Details: ONLY THE KNOB DOMAIN, AFTER TEV CLEAVAGE OF A HIS-TAGGED PROTEIN CONSTRUCT Source: (gene. exp.) HUMAN ADENOVIRUS TYPE 37 / Strain: P / Plasmid: PPROEX HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q64823 |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 533 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED MUTATION IN CHAINS A, B, C, TYR 173 TO ALA 173 ENGINEERED MUTATION IN CHAINS A, B, C, ...ENGINEERED |
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Sequence details | THE FIRST FIVE RESIDUES HAVE BEEN CHANGED IN ORDER TO INTRODUCE THE TEV CLEAVAGE SITE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49 % |
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Crystal grow | pH: 7.5 Details: RESERVOIR: 24 % PEG8000, 50 MM ZINC ACETATE, 100 MM HEPES, PROTEIN: 30 MM TRIS-HCL, PH 7.5, 150 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 9, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.18 Å / Num. obs: 87661 / % possible obs: 92.3 % / Redundancy: 3.33 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.059 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.21 / % possible all: 66.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QHV Resolution: 1.5→45.18 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE ELECTRON DENSITY THAT IS ASSOCIATED WITH THE ACETATE IONS IS POORLY DEFINED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.02 Å2 / ksol: 0.393 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.81 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→45.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
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Xplor file |
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