+Open data
-Basic information
Entry | Database: PDB / ID: 3esv | ||||||
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Title | Crystal structure of the engineered neutralizing antibody M18 | ||||||
Components | Antibody M18 light chain and antibody M18 heavy chain linked with a synthetic (GGGGS)4 linker | ||||||
Keywords | IMMUNE SYSTEM / single-chain FV / monoclonal antibody / immunoglobulin | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Monzingo, A.F. / Leysath, C.E. / Barnett, J. / Iverson, B.L. / Georgiou, G. / Robertus, J.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure of the engineered neutralizing antibody m18 complexed to domain 4 of the anthrax protective antigen. Authors: Leysath, C.E. / Monzingo, A.F. / Maynard, J.A. / Barnett, J. / Georgiou, G. / Iverson, B.L. / Robertus, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3esv.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esv.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 3esv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3esv_validation.pdf.gz | 440.9 KB | Display | wwPDB validaton report |
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Full document | 3esv_full_validation.pdf.gz | 447.3 KB | Display | |
Data in XML | 3esv_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3esv_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esv ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esv | HTTPS FTP |
-Related structure data
Related structure data | 3esuSC 3et9C 3etbC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Asymmetric unit contains two biological units. |
-Components
#1: Antibody | Mass: 26866.584 Da / Num. of mol.: 2 Mutation: I21V, L46F, S56P, S76N, Q78L, L94P, S1030N, T1058S, K1065E, T1069I Source method: isolated from a genetically manipulated source Details: periplasm / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): Jude-1 #2: Water | ChemComp-HOH / | Sequence details | RESIDUE NUMBERS FOR ANTIBODY M18 HEAVY CHAIN FRAGMENT HAVE OFFSET 1000 TO DISTINGUISH THEM FROM THE ...RESIDUE NUMBERS FOR ANTIBODY M18 HEAVY CHAIN FRAGMENT HAVE OFFSET 1000 TO DISTINGUIS | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20% PEG 4000, 0.1 M HEPES, 10% Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 24, 2004 / Details: blue max-flux confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 26245 / Num. obs: 26245 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Χ2: 0.968 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.107 / Num. unique all: 2514 / Χ2: 1.017 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3ESU Resolution: 2→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.865 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 52.192 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.87 Å2 / Biso mean: 17.324 Å2 / Biso min: 6.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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