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- PDB-3ls5: Anti-tetrahydrocannabinol Fab Fragment, Free Form -

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Basic information

Entry
Database: PDB / ID: 3ls5
TitleAnti-tetrahydrocannabinol Fab Fragment, Free Form
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
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)46,7182
Polymers46,7182
Non-polymers00
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-29 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.434, 121.434, 73.499
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 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

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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: 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 shellResolution: 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

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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 / 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
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2190 5 %RANDOM
Rwork0.214 ---
obs0.215 41609 99.97 %-
all-43799 --
Solvent computationShrinkage 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 parametersBiso max: 106.29 Å2 / Biso mean: 34.217 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 0 260 3538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133367
X-RAY DIFFRACTIONf_angle_d1.4654584
X-RAY DIFFRACTIONf_chiral_restr0.099531
X-RAY DIFFRACTIONf_plane_restr0.009581
X-RAY DIFFRACTIONf_dihedral_angle_d16.8541185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.9410.2981350.24425672702
1.941-1.9870.2991340.24225592693
1.987-2.0360.2991350.2325512686
2.036-2.0910.2481350.22525692704
2.091-2.1530.2751340.21625532687
2.153-2.2220.2581360.21725802716
2.222-2.3020.2781350.2225692704
2.302-2.3940.281350.21925672702
2.394-2.5030.2781360.22825752711
2.503-2.6350.2731370.22526042741
2.635-2.80.2541360.22725822718
2.8-3.0160.2751370.22326102747
3.016-3.3190.2411380.2226142752
3.319-3.7990.2521380.20826342772
3.799-4.7860.1841410.17826692810
4.786-42.9440.1911480.20228062954

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