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- PDB-1ynk: Identification of Key residues of the NC6.8 Fab antibody fragment... -

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Basic information

Entry
Database: PDB / ID: 1ynk
TitleIdentification of Key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeteners: Crystal structure of NC6.8 co-crystalized with high potency sweetener compound SC45647
Components
  • Ig gamma heavy chain
  • immunoglobulin kappa light chain
KeywordsIMMUNE SYSTEM / Sweetener compound / SC45657 and NC174
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SC5 / Kappa light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGokulan, K. / Khare, S. / Ronning, D.R. / Linthicum, S.D. / Sacchettini, J.C. / Rupp, B.
CitationJournal: Biochemistry / Year: 2005
Title: Cocrystal Structures of NC6.8 Fab Identify Key Interactions for High Potency Sweetener Recognition: Implications for the Design of Synthetic Sweeteners
Authors: Gokulan, K. / Khare, S. / Ronning, D.R. / Linthicum, S.D. / Sacchettini, J.C. / Rupp, B.
History
DepositionJan 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 2023Group: 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: immunoglobulin kappa light chain
H: Ig gamma heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8093
Polymers47,4792
Non-polymers3301
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-24 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.600, 48.190, 75.350
Angle α, β, γ (deg.)90.00, 109.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody immunoglobulin kappa light chain / NC6.8 Fab fragment L-chain / monoclonal antibody Fab fragment


Mass: 24123.807 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) / References: UniProt: A2P1G9*PLUS
#2: Antibody Ig gamma heavy chain / NC6.8 Fab fragment H-chain


Mass: 23355.021 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) / References: UniProt: Q6PJB2
#3: Chemical ChemComp-SC5 / 2-[((R)-{[4-(AMINOMETHYL)PHENYL]AMINO}{[(1R)-1-PHENYLETHYL]AMINO}METHYL)AMINO]ETHANE-1,1-DIOL / SC45647


Mass: 330.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 291 K / pH: 9.2
Details: 50 mM potassium hydrogen phosphate, 20% polyethylene glycol, pH 9.2, EVAPORATION, temperature 18C, pH 9.20, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→23.64 Å / Num. obs: 24844 / Observed criterion σ(I): 2.85 / Rmerge(I) obs: 0.3217 / Net I/σ(I): 8.8
Reflection shellHighest resolution: 2.1 Å / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
shake& Warpmodel building
REFMAC5.1refinement
HKL-2000data reduction
SnBphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGS

1cgs


Resolution: 2.1→23.64 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.769 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1246 5 %RANDOM
Rwork0.213 ---
obs0.216 23597 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å23.79 Å2
2---2.75 Å20 Å2
3---4.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 24 126 3495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223459
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4591.9614711
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6815436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05423.864132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.421515
X-RAY DIFFRACTIONr_chiral_restr0.1550.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022615
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.21707
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.22340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.86252221
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47973539
X-RAY DIFFRACTIONr_scbond_it1.67791455
X-RAY DIFFRACTIONr_scangle_it2.408111172
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 69 -
Rwork0.272 1152 -
obs--62.33 %

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