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- PDB-6xuk: AbLIFT design 15 of Ab 1116NS19.9 -

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Basic information

Entry
Database: PDB / ID: 6xuk
TitleAbLIFT design 15 of Ab 1116NS19.9
Components
  • Heavy chain
  • Light chain
KeywordsANTITUMOR PROTEIN / pancreatic cancer / diagnosis / in-silico optimized antibody / CA19-9 binder / immunotherapeutic reagent
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDiskin, R. / Borenstein-Katz, A.
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies.
Authors: Borenstein-Katz, A. / Warszawski, S. / Amon, R. / Eilon, M. / Cohen-Dvashi, H. / Leviatan Ben-Arye, S. / Tasnima, N. / Yu, H. / Chen, X. / Padler-Karavani, V. / Fleishman, S.J. / Diskin, R.
History
DepositionJan 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 29, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Mar 8, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.4Feb 7, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5705
Polymers47,5652
Non-polymers1,0053
Water11,908661
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-10 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.936, 64.936, 244.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-674-

HOH

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Components

#1: Antibody Heavy chain


Mass: 23751.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody Light chain /


Mass: 23813.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 820.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-2-3-4/a3-b1_a4-d1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 661 / 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: 2.71 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Ammonium citrate, Immidazole pH7, PEG 2K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97371 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97371 Å / Relative weight: 1
ReflectionResolution: 1.42→62.754 Å / Num. obs: 99787 / % possible obs: 100 % / Redundancy: 6.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.4 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.42-1.461.0663887472410.5580.491.1791.199.7
6.35-62.750.05727913520.9950.0240.05619.5100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7W

3u7w


Resolution: 1.42→62.754 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1846 5022 5.04 %
Rwork0.1487 --
obs0.1505 99620 99.89 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 118.18 Å2 / Biso mean: 23.7146 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.42→62.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 134 661 4089
Biso mean--27.03 34.2 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.42-1.43610.30871620.2649308299
1.4361-1.4530.3161550.24183077100
1.453-1.47070.29121360.2153150100
1.4707-1.48940.27831840.21163062100
1.4894-1.5090.26161770.19173123100
1.509-1.52960.24631540.17933096100
1.5296-1.55150.22361490.16543130100
1.5515-1.57460.22191620.16283086100
1.5746-1.59930.19971590.1553115100
1.5993-1.62550.19611730.15643119100
1.6255-1.65350.22151620.15043093100
1.6535-1.68360.20611660.1453132100
1.6836-1.7160.20131630.13913136100
1.716-1.7510.18651640.14023133100
1.751-1.78910.20051440.13743126100
1.7891-1.83070.19011990.14233092100
1.8307-1.87650.19611560.14093133100
1.8765-1.92720.1611610.13193143100
1.9272-1.98390.16121680.12963151100
1.9839-2.0480.12841660.12593142100
2.048-2.12120.17631830.12983128100
2.1212-2.20610.17041660.13183159100
2.2061-2.30650.18541850.13043173100
2.3065-2.42810.16971760.13463149100
2.4281-2.58020.17561650.13693191100
2.5802-2.77950.16251790.14193198100
2.7795-3.05920.20031740.15133223100
3.0592-3.50180.18051720.14413239100
3.5018-4.41170.16081800.13933297100
4.4117-62.7540.19741820.18293520100

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