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Yorodumi- PDB-3esu: Crystal structure of anthrax-neutralizing single-chain antibody 14b7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 3esu | ||||||||||||||||||||
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Title | Crystal structure of anthrax-neutralizing single-chain antibody 14b7 | ||||||||||||||||||||
Components | Antibody 14b7*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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | Authors | Monzingo, A.F. / Maynard, J.A. / 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 | 3esu.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3esu.ent.gz | 43.9 KB | Display | PDB format |
PDBx/mmJSON format | 3esu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3esu_validation.pdf.gz | 428.2 KB | Display | wwPDB validaton report |
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Full document | 3esu_full_validation.pdf.gz | 430.8 KB | Display | |
Data in XML | 3esu_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3esu_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/3esu ftp://data.pdbj.org/pub/pdb/validation_reports/es/3esu | HTTPS FTP |
-Related structure data
Related structure data | 3esvC 3et9C 3etbC 1forS 1jv5S 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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Details | Asymmetric unit contains one biological unit |
-Components
#1: Antibody | Mass: 26561.275 Da / Num. of mol.: 1 / Mutation: Q3V, M4L, T5I, Q78L, K107R, L1045P 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 |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUE NUMBERS FOR ANTIBODY 14B7* HEAVY CHAIN FRAGMENT OF ENTITY 1 HAVE OFFSET 1000 TO DISTINGUISH ...RESIDUE NUMBERS FOR ANTIBODY 14B7* HEAVY CHAIN FRAGMENT OF ENTITY 1 HAVE OFFSET 1000 TO DISTINGUIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.05 % |
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Crystal grow | Temperature: 298 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 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9641 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9641 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 54301 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Rmerge(I) obs: 0.079 / Χ2: 1.455 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.3→1.35 Å / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5384 / Χ2: 0.825 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 1JV5, 1FOR Resolution: 1.3→20 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.86 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 36.343 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 24.24 Å2 / Biso mean: 11.318 Å2 / Biso min: 4.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→20 Å
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Refine LS restraints |
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Xplor file |
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