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Yorodumi- PDB-4lar: Crystal structure of a therapeutic single chain antibody in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lar | |||||||||
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Title | Crystal structure of a therapeutic single chain antibody in complex with amphetamine | |||||||||
Components | Single chain antibody fragment scFv6H4 | |||||||||
Keywords | IMMUNE SYSTEM / methamphetamine / anti-methamphetamine antibody / therapeutic antibody / scFv | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2S)-1-phenylpropan-2-amine Function and homology information | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | |||||||||
Authors | Celical, R. / Gokulan, K. / Peterson, E.C. / Varughese, K.I. | |||||||||
Citation | Journal: Plos One / Year: 2013 Title: Structural characterization of a therapeutic anti-methamphetamine antibody fragment: oligomerization and binding of active metabolites. Authors: Peterson, E.C. / Celikel, R. / Gokulan, K. / Varughese, K.I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lar.cif.gz | 60 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lar.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lar.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lar_validation.pdf.gz | 446.8 KB | Display | wwPDB validaton report |
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Full document | 4lar_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 4lar_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 4lar_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4lar ftp://data.pdbj.org/pub/pdb/validation_reports/la/4lar | HTTPS FTP |
-Related structure data
Related structure data | 4laqC 4lasC 3gk2S 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
#1: Antibody | Mass: 26792.344 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPICZ-ALPHA / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H |
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#2: Chemical | ChemComp-1WE / ( |
#3: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 42.56 % |
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Crystal grow | Temperature: 287.1 K / pH: 7.8 Details: 1.15M sodium citrate, 0.28M imidazole-malate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 287.1K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→50 Å / Num. obs: 7947 / % possible obs: 93.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.093 / Rsym value: 0.04 / Net I/σ(I): 24.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GK2 Resolution: 2.38→48.03 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.832 / SU B: 11.164 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.531 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→48.03 Å
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Refine LS restraints |
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