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Yorodumi- PDB-4m1g: Structure of murine IgG2a A27D7-Fab in complex with vaccinia anti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m1g | ||||||
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Title | Structure of murine IgG2a A27D7-Fab in complex with vaccinia antigen A33R at the resolution of 1.6 Angstroms | ||||||
Components |
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Keywords | IMMUNE SYSTEM / IGG DOMAIN / ANTIBODY-ANTIGEN COMPLEX / FV / CH1 / IGG2A / ANTIGEN-BINDING FRAGMENT (FAB) / A33R ANTIGEN / PAPAIN DIGEST OF THE MAB / EEV MEMBRANE (OUTER MEMBRANE OF VACCINIA EV FORM) | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Matho, M.H. / Schlossman, A.M. / Zajonc, D.M. | ||||||
Citation | Journal: Plos Pathog. / Year: 2015 Title: Structural and Functional Characterization of Anti-A33 Antibodies Reveal a Potent Cross-Species Orthopoxviruses Neutralizer. Authors: Matho, M.H. / Schlossman, A. / Meng, X. / Benhnia, M.R. / Kaever, T. / Buller, M. / Doronin, K. / Parker, S. / Peters, B. / Crotty, S. / Xiang, Y. / Zajonc, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m1g.cif.gz | 137.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m1g.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 4m1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4m1g_validation.pdf.gz | 458.1 KB | Display | wwPDB validaton report |
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Full document | 4m1g_full_validation.pdf.gz | 461.1 KB | Display | |
Data in XML | 4m1g_validation.xml.gz | 27.2 KB | Display | |
Data in CIF | 4m1g_validation.cif.gz | 39.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/4m1g ftp://data.pdbj.org/pub/pdb/validation_reports/m1/4m1g | HTTPS FTP |
-Related structure data
Related structure data | 4lqfC 4lu5C 3k7bS 3ls4S 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 on special symmetry positions |
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-Components
#1: Antibody | Mass: 23410.865 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C B-cell Description: Fusion of SP2/0 myeloma cell line with splenocytes Cell: HYBRIDOMA / Production host: Mus musculus (house mouse) | ||||
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#2: Antibody | Mass: 23358.178 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C B-cell Description: Fusion of SP2/0 myeloma cell line with splenocytes Cell: HYBRIDOMA / Production host: Mus musculus (house mouse) | ||||
#3: Protein | Mass: 11049.040 Da / Num. of mol.: 2 / Fragment: ectodomain (UNP residues 89-185) / Mutation: S89M, L118M, K123A, L140M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Plasmid: pNAN::A33 (90-185) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q71TT1 #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M sodium cacodylate, 0.2M NaCl, 2.0M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2013 Details: Monochromator Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs, Crystal Type Si(111), Mirrors Rh coated flat mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→47.51 Å / Num. all: 87943 / Num. obs: 87767 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.652 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 3LS4, 3K7B Resolution: 1.6→44.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.602 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.517 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→44.51 Å
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Refine LS restraints |
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