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

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Basic information

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


immune response / extracellular space
Similarity search - Function
: / : / 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 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-NES / Kappa light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 19, 2016Group: Refinement description
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
L: Ig gamma light chain
H: Ig gamma heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7263
Polymers47,4972
Non-polymers2291
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-28 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.226, 48.140, 76.090
Angle α, β, γ (deg.)90.00, 109.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Ig gamma light 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) / References: UniProt: A2P1G9*PLUS
#2: Antibody Ig gamma heavy chain


Mass: 23373.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: Q6PJB2
#3: Chemical ChemComp-NES / 2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID


Mass: 229.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO6S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 9.2
Details: 50 mM potassium hydrogen phosphate, 20% polyethylene glycol, pH 9.2, EVAPORATION, temperature 18K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
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: 1.7→23.25 Å / Num. obs: 43252
Reflection shellResolution: 1.7→1.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→23.3 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.127 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24076 2217 5.1 %RANDOM
Rwork0.20673 ---
obs0.20848 41030 84.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å21.39 Å2
2---0.11 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 14 347 3699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223441
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9574690
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7155436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55823.846130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83915541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7641514
X-RAY DIFFRACTIONr_chiral_restr0.1250.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022585
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21517
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22336
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.73852225
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22173538
X-RAY DIFFRACTIONr_scbond_it1.47991401
X-RAY DIFFRACTIONr_scangle_it2.105111152
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 105 -
Rwork0.232 2140 -
obs--60.25 %

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