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- PDB-2yk1: Structure of human anti-nicotine Fab fragment in complex with nicotine -

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Basic information

Entry
Database: PDB / ID: 2yk1
TitleStructure of human anti-nicotine Fab fragment in complex with nicotine
Components
  • FAB FRAGMENT, HEAVY CHAIN
  • FAB FRAGMENT, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / MONOCLONAL ANTIBODIES / ANTI-SMOKING VACCINE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTars, K. / Kotelovica, S. / Lipowsky, G. / Bauer, M. / Beerli, R. / Bachmann, M. / Maurer, P.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Different Binding Modes of Free and Carrier-Protein-Coupled Nicotine in a Human Monoclonal Antibody.
Authors: Tars, K. / Kotelovica, S. / Lipowsky, G. / Bauer, M. / Beerli, R. / Bachmann, M. / Maurer, P.
History
DepositionMay 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Other
Revision 1.2Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAB FRAGMENT, HEAVY CHAIN
L: FAB FRAGMENT, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4353
Polymers45,2732
Non-polymers1621
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-12.7 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.110, 78.870, 75.470
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-2073-

HOH

21L-2066-

HOH

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Components

#1: Antibody FAB FRAGMENT, HEAVY CHAIN


Mass: 22297.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
#2: Antibody FAB FRAGMENT, LIGHT CHAIN


Mass: 22976.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human)
#3: Chemical ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE


Mass: 162.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: SITTING DROP, 5% PEG 3000, 0.1 M MES PH 6.0, 30% (V/V) PEG 200, 10 MG/ML PROTEIN, 20 MM NICOTINE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 26, 2008 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 34228 / % possible obs: 95 % / Observed criterion σ(I): 1.8 / Redundancy: 2.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.4
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 1.8 / % possible all: 91.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BOS

2bos


Resolution: 1.85→27.35 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.491 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26434 1635 5.1 %RANDOM
Rwork0.22446 ---
obs0.22648 30695 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.11 Å2
2---0.47 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.85→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 12 244 3012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.9643911
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43724.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54215423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.866159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212125
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.571.51843
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04922981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42131016
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1424.5927
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 123 -
Rwork0.308 2107 -
obs--87.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.74690.7128-0.27012.05090.12830.26890.0452-0.0487-0.06160.036-0.0501-0.17930.00880.01220.0050.05250.003200.10750.0170.0801-22.225-11.542-1.479
20.3495-0.51111.14524.9534-0.55017.1853-0.03710.106-0.0442-0.55310.18810.08780.2045-0.4278-0.15110.2107-0.2276-0.04760.32780.02550.0507-35.594-14.018-36.375
30.58610.21380.21321.0148-0.12991.76870.06380.00010.04890.02270.02560.0401-0.0984-0.0314-0.08940.07550.00150.04170.0764-0.00330.0657-22.0358.89-7.56
42.7371.8791-1.14944.2585-1.23863.7619-0.00790.11120.0885-0.2230.46230.4746-0.1917-0.9174-0.45450.0450.0438-0.00930.33360.17090.115-37.4442.383-28.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L5 - 106A
2X-RAY DIFFRACTION2L107 - 205
3X-RAY DIFFRACTION3H5 - 112
4X-RAY DIFFRACTION4H113 - 207

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