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- PDB-6kx0: Crystal structure of SN-101 mAb non-liganded form -

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Basic information

Entry
Database: PDB / ID: 6kx0
TitleCrystal structure of SN-101 mAb non-liganded form
Components
  • Fab Fragment-SN-101-Heavy chain
  • Fab Fragment-SN-101-Light chain
KeywordsIMMUNE SYSTEM / Antibody / IgG1 / MUC1 / Glycopeptide
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.404 Å
AuthorsWakui, H. / Tanaka, Y. / Kato, K. / Ose, T. / Matsumoto, I. / Min, Y. / Tachibana, T. / Nishimura, S.-I.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25220206 Japan
Japan Society for the Promotion of Science19H00918 Japan
CitationJournal: Chem Sci / Year: 2020
Title: A straightforward approach to antibodies recognising cancer specific glycopeptidic neoepitopes
Authors: Wakui, H. / Tanaka, Y. / Ose, T. / Matsumoto, I. / Kato, K. / Min, Y. / Tachibana, T. / Sato, M. / Naruchi, K. / Martin, F.G. / Hinou, H. / Nishimura, S.-I.
History
DepositionSep 9, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 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

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Assembly

Deposited unit
A: Fab Fragment-SN-101-Heavy chain
B: Fab Fragment-SN-101-Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2254
Polymers51,9802
Non-polymers2442
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-18 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.860, 40.100, 67.780
Angle α, β, γ (deg.)90.000, 99.830, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Antibody Fab Fragment-SN-101-Heavy chain


Mass: 25541.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab Fragment-SN-101-Light chain


Mass: 26438.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 300-350 mM NaSCN 20-30% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 16818 / % possible obs: 99.6 % / Redundancy: 4.99 % / Rrim(I) all: 0.101 / Net I/σ(I): 12.78
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 5.08 % / Num. unique obs: 2665 / Rrim(I) all: 0.663 / % possible all: 98.9

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PZ5

1pz5


Resolution: 2.404→39.378 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2779 842 5.01 %
Rwork0.2254 --
obs0.2278 16816 99.68 %
Displacement parametersBiso mean: 51.59 Å2
Refinement stepCycle: LAST / Resolution: 2.404→39.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 16 37 3348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033392
X-RAY DIFFRACTIONf_angle_d0.6264618
X-RAY DIFFRACTIONf_chiral_restr0.0413515
X-RAY DIFFRACTIONf_plane_restr0.0042586
X-RAY DIFFRACTIONf_dihedral_angle_d11.24282017

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