[English] 日本語
Yorodumi- PDB-5eor: Structure of the murine antibody Fab 8E3 bound to the vaccinia vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eor | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the murine antibody Fab 8E3 bound to the vaccinia virus A27 peptide 101-110 | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / antibody / Fab / vaccinia virus / neutralizing / linear epitope / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Chordopoxvirus fusion protein/multifunctional envelope protein A27 / Chordopoxvirus multifunctional envelope protein A27 / fusion of virus membrane with host plasma membrane / Immunoglobulins / viral envelope / Immunoglobulin-like / Sandwich / Mainly Beta / Protein OPG154 Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å | ||||||
Authors | Matho, M.H. / Zajonc, D.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Virol. / Year: 2016 Title: Linear Epitopes in Vaccinia Virus A27 Are Targets of Protective Antibodies Induced by Vaccination against Smallpox. Authors: Kaever, T. / Matho, M.H. / Meng, X. / Crickard, L. / Schlossman, A. / Xiang, Y. / Crotty, S. / Peters, B. / Zajonc, D.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5eor.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5eor.ent.gz | 76.9 KB | Display | PDB format |
PDBx/mmJSON format | 5eor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eor_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5eor_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 5eor_validation.xml.gz | 19 KB | Display | |
Data in CIF | 5eor_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/5eor ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eor | HTTPS FTP |
-Related structure data
Related structure data | 5eoqC 2ntfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23028.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
---|---|
#2: Antibody | Mass: 23471.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) |
#3: Protein/peptide | Mass: 1222.308 Da / Num. of mol.: 1 / Fragment: UNP residues 101-110 / Source method: obtained synthetically / Source: (synth.) Vaccinia virus / References: UniProt: P11258*PLUS |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.23 Å3/Da / Density % sol: 70.9 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% PEG 3000, 200 mM magnesium chloride, 100 mM cacodylate ph 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→55.62 Å / Num. obs: 35641 / % possible obs: 97.8 % / Redundancy: 2.5 % / Rsym value: 0.095 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.27→2.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.1 / % possible all: 98.1 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NTF Resolution: 2.27→55.62 Å / SU B: 4.657 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.313 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→55.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|