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Yorodumi- PDB-3ls4: Crystal Structure of Anti-tetrahydrocannabinol Fab Fragment in Co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ls4 | ||||||
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Title | Crystal Structure of Anti-tetrahydrocannabinol Fab Fragment in Complex with THC | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Immunoglobulin / Fab fragment / Cannabinoid complex | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-TCI Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Niemi, M.H. / Rouvinen, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: A structural insight into the molecular recognition of a (-)-Delta9-tetrahydrocannabinol and the development of a sensitive, one-step, homogeneous immunocomplex-based assay for its detection Authors: Niemi, M.H. / Turunen, L. / Pulli, T. / Nevanen, T.K. / Hoyhtya, M. / Soderlund, H. / Rouvinen, J. / Takkinen, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ls4.cif.gz | 101.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ls4.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ls4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ls4_validation.pdf.gz | 851.7 KB | Display | wwPDB validaton report |
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Full document | 3ls4_full_validation.pdf.gz | 860.5 KB | Display | |
Data in XML | 3ls4_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3ls4_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/3ls4 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3ls4 | 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: 23346.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 23371.443 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Chemical | ChemComp-TCI / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12% PEG 3350, 0.1M sodium Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Monochromator: Si (111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 38385 / Num. obs: 38070 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 36.28 Å2 / Rsym value: 0.039 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 5138 / Rsym value: 0.445 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Free form structure of the same antibody Resolution: 2→35.731 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.791 / SU ML: 0.32 / σ(F): 2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.962 Å2 / ksol: 0.337 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.43 Å2 / Biso mean: 39.22 Å2 / Biso min: 19.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2→35.731 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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