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- PDB-6xun: Ab 5b1 bound to CA19-9 -

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Basic information

Entry
Database: PDB / ID: 6xun
TitleAb 5b1 bound to CA19-9
Components
  • Heavy chain
  • Light chain
KeywordsANTITUMOR PROTEIN / Pancreatic cancer / CA19-9 binder / Diagnosis / Immunotherapy reagent / Immunotheraeutic agent
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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: Database references / Category: citation / citation_author / database_2
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 1.3Jan 24, 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

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Assembly

Deposited unit
H: Heavy chain
B: Light chain
D: Light chain
L: Light chain
A: Heavy chain
C: Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,87113
Polymers145,0406
Non-polymers2,8317
Water8,737485
1
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1673
Polymers48,3472
Non-polymers8211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-3 kcal/mol
Surface area19260 Å2
MethodPISA
2
B: Light chain
A: Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3525
Polymers48,3472
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-0 kcal/mol
Surface area19040 Å2
MethodPISA
3
D: Light chain
C: Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3525
Polymers48,3472
Non-polymers1,0053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-5 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.540, 152.540, 60.887
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody Heavy chain


Mass: 24823.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain /


Mass: 23522.887 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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.: 3
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.: 4
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: NaCl, Bis tris propane pH9, PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873313 Å / Relative weight: 1
ReflectionResolution: 2.41→47.584 Å / Num. obs: 61056 / % possible obs: 99.8 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.068 / Rrim(I) all: 0.155 / Net I/σ(I): 9.3
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
2.41-2.495.11.0932983658940.5080.531.2161.498.1
9.33-47.5850.034519910450.9990.0170.03834.198.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XTG

6xtg


Resolution: 2.41→47.584 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.91
RfactorNum. reflection% reflection
Rfree0.2147 2006 3.29 %
Rwork0.1693 --
obs0.1708 61028 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 116.76 Å2 / Biso mean: 45.3005 Å2 / Biso min: 18.97 Å2
Refinement stepCycle: final / Resolution: 2.41→47.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9963 0 192 485 10640
Biso mean--44.92 44.41 -
Num. residues----1310
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4105-2.47080.34471380.2822411697
2.4708-2.53760.32231490.24174254100
2.5376-2.61220.27511360.22934197100
2.6122-2.69650.27691380.21994232100
2.6965-2.79290.29381500.21384267100
2.7929-2.90470.27441440.20664196100
2.9047-3.03690.28531420.19934249100
3.0369-3.1970.20091520.18554196100
3.197-3.39720.23171380.17754200100
3.3972-3.65940.20711430.16664227100
3.6594-4.02750.19961400.15274244100
4.0275-4.60990.191460.1264210100
4.6099-5.80630.16621510.13134215100
5.8063-47.5840.15391390.15084219100

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