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Yorodumi- PDB-4lu5: Structure of murine IgG2a A20G2-Fab in complex with vaccinia anti... -
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-Basic information
Entry | Database: PDB / ID: 4lu5 | ||||||
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Title | Structure of murine IgG2a A20G2-Fab in complex with vaccinia antigen A33R at the resolution of 2.9 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 | Vaccinia virus Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 | 4lu5.cif.gz | 201.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lu5.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lu5_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 4lu5_full_validation.pdf.gz | 471.5 KB | Display | |
Data in XML | 4lu5_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 4lu5_validation.cif.gz | 49.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/4lu5 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/4lu5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: 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 #2: Antibody | Mass: 23134.998 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C Description: musculus B-cell Fusion of SP2/0 myeloma cell line with splenocytes Cell: Hybridoma / Production host: Mus musculus (house mouse) #3: Antibody | Mass: 24166.971 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C Description: musculus B-cell Fusion of SP2/0 myeloma cell line with splenocytes Cell: Hybridoma / Production host: Mus musculus (house mouse) #4: Water | ChemComp-HOH / | Sequence details | AUTHORS PROVIDED SEQUENCE DATABASE REFERENCES: A20G2 ANTIBODY HEAVY CHAIN GI 563323196, ACCESSION ...AUTHORS PROVIDED SEQUENCE DATABASE REFERENCES | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG3350 (w/v), 8% tacsimate (v/v), pH 7.0, 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: 2.9→54.94 Å / Num. all: 31632 / Num. obs: 30937 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.228 / Rsym value: 0.228 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.751 / Mean I/σ(I) obs: 2 / Rsym value: 0.751 / % possible all: 93.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→54.94 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.849 / SU B: 18.615 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / 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: 37.655 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→54.94 Å
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