+Open data
-Basic information
Entry | Database: PDB / ID: 3gm0 | ||||||
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Title | Anti-methamphetamine single chain Fv in complex with MDMA | ||||||
Components | anti-methamphetamine single chain Fv | ||||||
Keywords | IMMUNE SYSTEM / anti-methamphetamine antibody / single chain Fv / Therapeutic antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-B41 Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Celikel, R. / Peterson, E.C. / Owens, M. / Varughese, K.I. | ||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Crystal structures of a therapeutic single chain antibody in complex with two drugs of abuse-Methamphetamine and 3,4-methylenedioxymethamphetamine. Authors: Celikel, R. / Peterson, E.C. / Owens, S.M. / 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 | 3gm0.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gm0.ent.gz | 43.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gm0_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 3gm0_full_validation.pdf.gz | 443.4 KB | Display | |
Data in XML | 3gm0_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 3gm0_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/3gm0 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/3gm0 | 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: Antibody | Mass: 27789.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG / Plasmid: pPICZ-alpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H |
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#2: Chemical | ChemComp-B41 / ( |
#3: Water | ChemComp-HOH / |
Sequence details | THE PROTEIN WAS CRYSTALLIZED AS A FUSION PROTEIN WHERE TWO CHAINS, CHAIN H AND CHAIN L, WERE FUSED ...THE PROTEIN WAS CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.35 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion / pH: 8.3 Details: 1.15M sodium Citrate, 0.28M Imidazole malate, pH 8.3, VAPOR DIFFUSION, temperature 287K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2008 / Details: single crystal bent monochromator |
Radiation | Monochromator: single crystal bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→32.4 Å / Num. all: 8316 / Num. obs: 8316 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 3.75 % / Rsym value: 0.045 |
Reflection shell | Resolution: 2.4→2.58 Å / Redundancy: 3.7 % / Rsym value: 0.21 / % possible all: 99.5 |
-Processing
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Refinement | Resolution: 2.4→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
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Solvent computation | Bsol: 66.944 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.68 Å2 / Biso mean: 39.042 Å2 / Biso min: 16.72 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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