[English] 日本語
Yorodumi- PDB-6app: Anti-Marburgvirus Nucleoprotein Single Domain Antibody A Complexe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6app | ||||||
---|---|---|---|---|---|---|---|
Title | Anti-Marburgvirus Nucleoprotein Single Domain Antibody A Complexed with Nucleoprotein C-terminal domain | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM | ||||||
Function / homology | Function and homology information viral RNA genome packaging / helical viral capsid / viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Lama glama (llama) Lake Victoria marburgvirus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Taylor, A.B. / Garza, J.A. | ||||||
Citation | Journal: Front Immunol / Year: 2017 Title: Unveiling a Drift Resistant Cryptotope withinMarburgvirusNucleoprotein Recognized by Llama Single-Domain Antibodies. Authors: Garza, J.A. / Taylor, A.B. / Sherwood, L.J. / Hart, P.J. / Hayhurst, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6app.cif.gz | 60 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6app.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 6app.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/6app ftp://data.pdbj.org/pub/pdb/validation_reports/ap/6app | HTTPS FTP |
---|
-Related structure data
Related structure data | 4w2oC 4w2pC 4w2qC 6apoSC 6apqC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 14215.889 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) Description: Semi-synthetic single pot library Nomad 1 based upon Lama glama Plasmid: PECAN73 / Production host: Escherichia coli (E. coli) |
---|---|
#2: Protein | Mass: 12238.336 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 601-695 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lake Victoria marburgvirus (strain Musoke-80) Strain: Musoke-80 / Gene: NP / Plasmid: pE-NP600 / Production host: Escherichia coli (E. coli) / References: UniProt: P27588 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.99 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 15% polyethylene glycol 6000, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→46.15 Å / Num. obs: 20487 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 19 Å2 / Rpim(I) all: 0.039 / Rsym value: 0.089 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2902 / Rpim(I) all: 0.281 / Rsym value: 0.64 / % possible all: 98.1 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6APO Resolution: 1.75→34.343 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.68
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→34.343 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|