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- PDB-3ls4: Crystal Structure of Anti-tetrahydrocannabinol Fab Fragment in Co... -

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Basic information

Entry
Database: PDB / ID: 3ls4
TitleCrystal Structure of Anti-tetrahydrocannabinol Fab Fragment in Complex with THC
Components
  • Heavy chain of antibody Fab fragment
  • Light chain of antibody Fab fragment
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin / Fab fragment / Cannabinoid complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-TCI
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNiemi, M.H. / Rouvinen, J.
CitationJournal: 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
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light chain of antibody Fab fragment
H: Heavy chain of antibody Fab fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0333
Polymers46,7182
Non-polymers3141
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-27 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.760, 122.760, 73.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Light chain of antibody Fab fragment


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)
#2: Antibody Heavy chain of antibody Fab fragment


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 / (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydro-6H-benzo[c]chromen-1-ol / Tetrahydrocannabinol / Tetrahydrocannabinol


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2009
RadiationMonochromator: Si (111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1904 5 %RANDOM
Rwork0.213 ---
obs0.216 36165 99.2 %-
all-38069 --
Solvent computationShrinkage 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 parametersBiso max: 79.43 Å2 / Biso mean: 39.22 Å2 / Biso min: 19.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.928 Å2-0 Å20 Å2
2---2.928 Å2-0 Å2
3---5.856 Å2
Refinement stepCycle: LAST / Resolution: 2→35.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 23 240 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123408
X-RAY DIFFRACTIONf_angle_d1.5844644
X-RAY DIFFRACTIONf_chiral_restr0.106538
X-RAY DIFFRACTIONf_plane_restr0.007586
X-RAY DIFFRACTIONf_dihedral_angle_d17.7821208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.3471350.27525582693100
2.05-2.1050.3371350.26825612696100
2.105-2.1670.3521350.26525702705100
2.167-2.2370.3441330.26625402673100
2.237-2.3170.2781360.25825772713100
2.317-2.410.3511350.25725662701100
2.41-2.520.3331360.25225902726100
2.52-2.6520.2821350.25525592694100
2.652-2.8190.3011360.25125792715100
2.819-3.0360.2951360.23825952731100
3.036-3.3420.2731370.2212600273799
3.342-3.8250.2371370.192603274099
3.825-4.8170.1871390.1592633277299
4.817-35.7360.2121390.1712634277394

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