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- PDB-7u61: Crystal Structure of Anti-Nicotine Antibody NIC311 Fab Complexed ... -

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Basic information

Entry
Database: PDB / ID: 7u61
TitleCrystal Structure of Anti-Nicotine Antibody NIC311 Fab Complexed with Nicotine
Components
  • NIC311 Fab Heavy Chain
  • NIC311 Fab Light Chain
KeywordsIMMUNE SYSTEM / mAb
Function / homology(S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRodarte, J.V. / Pancera, M.P. / Liban, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Structure / Year: 2023
Title: Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding.
Authors: Rodarte, J.V. / Baehr, C. / Hicks, D. / Liban, T.L. / Weidle, C. / Rupert, P.B. / Jahan, R. / Wall, A. / McGuire, A.T. / Strong, R.K. / Runyon, S. / Pravetoni, M. / Pancera, M.
History
DepositionMar 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: NIC311 Fab Heavy Chain
L: NIC311 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3916
Polymers46,9412
Non-polymers4504
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-52 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.762, 71.326, 57.344
Angle α, β, γ (deg.)90.000, 107.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-423-

HOH

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Components

#1: Antibody NIC311 Fab Heavy Chain


Mass: 24107.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody NIC311 Fab Light Chain


Mass: 22833.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#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 / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: MES pH 5.5, 60mM PEG 4000, 15% Ammonium Sulfate, 90mM

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→59.74 Å / Num. obs: 27444 / % possible obs: 99 % / Redundancy: 2.8 % / Biso Wilson estimate: 34.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.036 / Rrim(I) all: 0.063 / Net I/σ(I): 23.5 / Num. measured all: 77729 / Scaling rejects: 4114
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.05-2.120.424362718320.8560.3410.5471.290.6
9.17-59.742.70.0148933360.9990.010.01894.199.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YK1

2yk1


Resolution: 2.1→54.68 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2636 1850 7.19 %
Rwork0.2304 23886 -
obs0.2328 25736 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.77 Å2 / Biso mean: 43.3249 Å2 / Biso min: 18.49 Å2
Refinement stepCycle: final / Resolution: 2.1→54.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 27 89 3303
Biso mean--60.32 41.05 -
Num. residues----425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.160.35331390.34161762190196
2.16-2.220.29521410.3091823196499
2.22-2.290.31851390.29561843198299
2.29-2.370.35721450.284518241969100
2.37-2.470.28891370.286918421979100
2.47-2.580.33861440.284718191963100
2.58-2.720.35521470.285418481995100
2.72-2.890.31871450.267618211966100
2.89-3.110.26631380.258618431981100
3.11-3.420.25411430.237418431986100
3.42-3.920.22111430.202618471990100
3.92-4.940.21051460.167218602006100
4.94-54.680.23561430.195919112054100

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