+Open data
-Basic information
Entry | Database: PDB / ID: 5mhr | ||||||
---|---|---|---|---|---|---|---|
Title | T3D reovirus sigma1 complexed with 9BG5 Fab fragments | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / reovirus sigma1 / virus antibody complex / neutralization / VIRAL PROTEIN | ||||||
Function / homology | Function and homology information virion component => GO:0044423 / cell adhesion / symbiont entry into host cell / virion attachment to host cell Similarity search - Function | ||||||
Biological species | Reovirus sp. Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Stehle, T. / Dietrich, M.H. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J. Virol. / Year: 2017 Title: Structural Insights into Reovirus sigma 1 Interactions with Two Neutralizing Antibodies. Authors: Dietrich, M.H. / Ogden, K.M. / Katen, S.P. / Reiss, K. / Sutherland, D.M. / Carnahan, R.H. / Goff, M. / Cooper, T. / Dermody, T.S. / Stehle, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5mhr.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5mhr.ent.gz | 947.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mhr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mhr_validation.pdf.gz | 524.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5mhr_full_validation.pdf.gz | 544.4 KB | Display | |
Data in XML | 5mhr_validation.xml.gz | 97.1 KB | Display | |
Data in CIF | 5mhr_validation.cif.gz | 131.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/5mhr ftp://data.pdbj.org/pub/pdb/validation_reports/mh/5mhr | HTTPS FTP |
-Related structure data
Related structure data | 5mhsC 1figS 2oj5S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 17921.033 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Reovirus sp. / Gene: S1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86335 #2: Antibody | Mass: 23282.822 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: DUE TO POORLY DEFINED ELECTRON DENSITY THE CONSTANT REGION OF THE FAB FRAGMENT WAS NOT BUILT FOR CHAIN J AND CHAIN L Source: (natural) Mus musculus (house mouse) #3: Antibody | Mass: 23527.369 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: DUE TO POORLY DEFINED ELECTRON DENSITY THE CONSTANT REGION OF THE FAB FRAGMENT WAS NOT BUILT FOR CHAIN K AND CHAIN M Source: (natural) Mus musculus (house mouse) |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.33 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 11% (w/v) PEG8000, 0.1 M Tris pH 7.0, 0.2 M magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.045 Å / Num. obs: 94667 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 55.9 Å2 / Net I/σ(I): 13.08 |
Reflection shell | Resolution: 3→3.08 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.89 / % possible all: 98.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OJ5 AND 1FIG Resolution: 3→49.05 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.66
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.05 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|