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- PDB-2ykl: Structure of human anti-nicotine Fab fragment in complex with nic... -

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Basic information

Entry
Database: PDB / ID: 2ykl
TitleStructure of human anti-nicotine Fab fragment in complex with nicotine-11-yl-methyl-(4-ethylamino-4-oxo)-butanoate
Components
  • FAB FRAGMENT, HEAVY CHAIN
  • FAB FRAGMENT, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / MONOCLONAL ANTIBODIES / ANTI-SMOKING VACCINE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-NLD
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 27, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)45,7253
Polymers45,4052
Non-polymers3191
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-21.9 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.240, 78.840, 73.690
Angle α, β, γ (deg.)90.00, 116.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-2036-

HOH

21L-2043-

HOH

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Components

#1: Antibody FAB FRAGMENT, HEAVY CHAIN


Mass: 22412.092 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: 22993.244 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-NLD / NICOTINE-11-YL-METHYL-(4-ETHYLAMINO-4-OXO)-BUTANOATE


Mass: 319.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsNICOTINE-11-YL-METHYL-(4-ETHYLAMINO-4-OXO)-BUTANOATE (NLD): LINKER PART IS DISORDERED BEYOND C18 ...NICOTINE-11-YL-METHYL-(4-ETHYLAMINO-4-OXO)-BUTANOATE (NLD): LINKER PART IS DISORDERED BEYOND C18 ATOM AND NOT INCLUDED IN THE MODEL

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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: 6.5
Details: SITTING DROP, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M MGCL2, 31% PEG MME 2000, 10 MG/ML PROTEIN, 20MM NICOTINE-11-YL-METHYL-(4-ETHYLAMINO-4-OXO)-BUTANOATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2010 / Details: BENT COLLIMATING MIRROR AND TOROID
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 22342 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YK1

2yk1


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.24 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27404 1124 5 %RANDOM
Rwork0.21352 ---
obs0.21658 21216 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.691 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å2-0.38 Å2
2---0.87 Å20 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2832 0 19 152 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9644006
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4885374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90524.18498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22615423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.185158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212184
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_it0.5421.51892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99923056
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.42931036
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2234.5950
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 74 -
Rwork0.227 1571 -
obs--100 %
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)
11.69091.09980.1753.54420.37120.62390.0261-0.04170.0054-0.0156-0.0415-0.21230.0207-0.02120.01530.07370.0120.05640.15550.01410.057-22.225-11.542-1.479
21.251-0.03360.87724.2541-0.4753.5128-0.03170.108-0.0883-0.33280.2549-0.21530.1303-0.246-0.22320.129-0.14550.02820.306900.0406-35.594-14.018-36.375
30.59360.3839-0.00361.172-0.27362.5212-0.0308-0.00050.1082-0.03390.06160.095-0.106-0.03-0.03070.09790.00470.05230.141-0.00440.0694-22.0358.89-7.56
43.39321.3598-1.14573.6629-1.24713.616-0.10150.25740.0711-0.11880.42320.46630.1442-0.8764-0.32170.1141-0.00980.01520.3220.08860.0873-37.4442.383-28.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L5 - 106A
2X-RAY DIFFRACTION2L107 - 208
3X-RAY DIFFRACTION3H5 - 112
4X-RAY DIFFRACTION4H113 - 208

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