+Open data
-Basic information
Entry | Database: PDB / ID: 3ls5 | ||||||
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Title | Anti-tetrahydrocannabinol Fab Fragment, Free Form | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody / Immunoglobulin / Fab fragment / Cannabinoid complex | ||||||
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: 1.9 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 | 3ls5.cif.gz | 96.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ls5.ent.gz | 77.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ls5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ls5_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 3ls5_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 3ls5_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 3ls5_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/3ls5 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3ls5 | 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: 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: 2.9 Å3/Da / Density % sol: 57.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 14% PEG 3350, 0.1 M sodium citrate, pH 5.2, 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: 1.9→50 Å / Num. all: 43817 / Num. obs: 43799 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.054 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 6159 / Rsym value: 0.386 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.933 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.833 / SU ML: 0.29 / σ(F): 2.01 / 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: 41.495 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.29 Å2 / Biso mean: 34.217 Å2 / Biso min: 12.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.933 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: 16 / % reflection obs: 100 %
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