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- PDB-6xtg: Ab 1116NS19.9 bound to CA19-9 -

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Basic information

Entry
Database: PDB / ID: 6xtg
TitleAb 1116NS19.9 bound to CA19-9
Components
  • Heavy chain
  • Light chain
KeywordsANTITUMOR PROTEIN / Pancreatic cancer / CA19-9 binder / Diagnosis / Immunotherapy reagent
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4034
Polymers47,5592
Non-polymers8442
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-14 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.169, 60.197, 84.436
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11H-535-

HOH

21H-545-

HOH

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Components

#1: Antibody Light chain /


Mass: 23759.486 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 Heavy chain


Mass: 23799.566 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)
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: n-Octyl-b-D-glucoside, Na citrate tri di pH 5.5, PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.55→44.585 Å / Num. obs: 64876 / % possible obs: 97.6 % / Redundancy: 5.5 % / Biso Wilson estimate: 27.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.025 / Rrim(I) all: 0.059 / Net I/σ(I): 13
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
1.55-1.65.81.4373565061960.5680.6511.581.196.3
6-44.5850.029629412620.9990.0140.03338.898.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u7w

3u7w


Resolution: 1.55→44.585 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.13
RfactorNum. reflection% reflection
Rfree0.2013 1988 3.07 %
Rwork0.1739 --
obs0.1747 64837 97.28 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 176.67 Å2 / Biso mean: 43.6823 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: final / Resolution: 1.55→44.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3292 0 107 382 3781
Biso mean--37.46 45.09 -
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 (%)
1.55-1.58880.3341320.3115438596
1.5888-1.63180.31071400.2976435696
1.6318-1.67980.32711420.2978440596
1.6798-1.7340.28661460.2874438396
1.734-1.7960.32331350.2506442497
1.796-1.86790.26591420.2181442297
1.8679-1.95290.23461380.1974447197
1.9529-2.05580.22111480.1837442097
2.0558-2.18460.21281420.177451698
2.1846-2.35330.22041370.1737453198
2.3533-2.59010.21521460.1777452998
2.5901-2.96480.18831440.1723457398
2.9648-3.73510.2021450.1594463598
3.7351-44.5850.15521510.1451479998
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.3247-5.1414-4.72733.39642.99033.6130.195-0.28130.8153-0.37090.442-0.636-0.42950.3783-0.84660.2660.0120.030.2471-0.01060.3279-9.06426.9789-13.1407
23.0465-1.8679-1.42392.2791.99312.7825-0.07-0.30550.42490.33730.3255-0.43260.32350.4659-0.35910.26460.0411-0.02910.3047-0.06290.3326-7.32580.5699-10.9663
33.4742-1.4893-0.72663.3129-0.12153.47040.0833-0.24090.26810.24510.1118-0.3192-0.2371-0.0891-0.2240.25810.0152-0.01370.2445-0.01460.3063-16.25536.6864-3.4811
46.38660.23630.28537.40221.86242.326-0.20751.2499-0.291-0.55470.09440.28150.7451-0.79280.00390.334-0.0448-0.0490.4568-0.04520.3614-23.5856-1.0588-15.7227
55.0485-0.9295-1.01897.32920.73076.6521-0.1209-0.5150.11060.96460.0139-0.26290.07260.17270.09870.3521-0.0024-0.06720.26040.00610.2195-16.8354-0.91012.8278
66.25321.60382.6934.41263.54644.8559-0.0487-0.45080.13960.3320.1741-0.42260.35330.3045-0.34680.34420.0494-0.04630.3006-0.01010.251-10.9282-1.6969-3.324
72.2886-1.8256-1.8952.63552.29713.36110.0764-0.08480.10490.0550.1053-0.25730.11620.1042-0.15930.22620.0108-0.02430.2254-0.00820.246-13.91371.0489-13.143
83.4773-2.09260.692.21270.8441.90420.15950.47320.6857-0.4628-0.5317-0.95490.16940.3320.2640.21870.05570.05280.30510.04040.3946-6.494911.46-40.2831
94.49844.9650.22236.3246-1.25632.65630.99850.56261.6978-1.2494-1.21-1.4212-0.63790.19980.1930.87080.1990.05261.38320.17430.9331-17.605728.2242-52.3307
101.9948-2.64621.59365.0261-1.96922.2548-0.26860.00680.38780.29640.1352-0.3537-0.3273-0.07380.12030.20450.0251-0.01770.2377-0.00170.3664-12.14215.2211-35.6527
112.4948-3.72873.43545.6134-5.30424.9791-0.25980.07281.03980.1849-0.4491-1.0192-0.3360.42120.61050.24830.0402-0.06970.26290.03420.5844-2.780516.4493-32.4674
125.3012-0.54415.20541.55350.48966.05150.10282.01750.8723-0.2374-0.5009-0.7906-1.10032.2780.27210.3857-0.06590.0620.67450.26390.7828-3.528321.9694-44.9567
134.27090.60974.03562.35290.92734.1340.1070.8361-1.4572-0.18670.69710.24250.6010.2275-0.86720.4056-0.113-0.05280.3199-0.05840.571-33.881-3.4755-8.3795
143.064-0.68741.23992.3111-2.72467.09630.08350.3664-0.0996-0.2267-0.07490.37780.0352-0.6478-0.01580.21250.0054-0.04720.3619-0.01870.3408-39.249813.7267-18.6714
152.913-0.058-0.21674.2333-1.26014.7609-0.0284-0.1842-0.45560.31790.03640.34540.307-0.51060.01510.1618-0.04780.01560.21010.0110.2778-33.94665.9318-5.7016
165.8232-5.2587-5.20364.93384.93464.9254-0.06291.0959-0.1247-0.2946-0.1971-0.1492-0.0834-0.4845-0.07960.2013-0.0360.00860.3814-0.00660.2547-23.512314.3215-14.4832
172.9876-0.70330.99212.85590.08733.1838-0.0118-0.0498-0.04410.1197-0.02360.2431-0.137-0.34660.01720.165-0.00970.00960.215-0.01690.2002-33.373814.5368-8.7414
184.0916-3.89465.20447.1212-6.49279.50670.1880.1528-0.3247-0.12890.04960.23490.4490.011-0.22680.208-0.0461-0.00130.2185-0.02520.31-30.15894.5274-13.0489
192.7378-3.2887-2.90664.53161.38876.67160.45840.12510.5811-0.4279-0.1478-0.5054-0.1670.2589-0.20430.2134-0.006-0.03170.2520.00710.2669-19.841717.4275-42.9451
203.491-3.2076-3.41035.39393.22745.5711-0.0326-0.0293-0.1643-0.1540.051-0.09710.47840.30940.14330.2530.0808-0.030.24810.04230.2201-23.538113.697-41.8195
213.75262.4079-0.85161.77130.02731.96490.39610.7645-0.2241-1.47-0.08170.50690.7709-0.4623-0.15240.70240.1241-0.1290.4654-0.02450.3296-23.70265.3745-52.906
224.2763-4.9096-3.50927.36184.22215.1715-0.0608-0.17290.0018-0.07210.1125-0.02460.11020.3144-0.0590.22860.032-0.04760.29270.01290.2991-22.213813.2391-37.3438
233.7966-2.4649-3.69423.44191.45865.68470.6791.0673-0.4213-0.8567-0.69290.09690.1192-0.1846-0.0220.59020.1676-0.06050.3664-0.04430.286-21.969811.0096-52.8708
246.1703-4.09480.28446.85620.26534.51210.76490.87611.2168-0.9758-0.5254-0.7332-0.5032-0.1218-0.30810.64390.23680.07550.49080.08250.2849-20.525217.1978-55.373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1:13)H1 - 13
2X-RAY DIFFRACTION2(chain H and resid 14:25)H14 - 25
3X-RAY DIFFRACTION3(chain H and resid 26:40)H26 - 40
4X-RAY DIFFRACTION4(chain H and resid 41:47)H41 - 47
5X-RAY DIFFRACTION5(chain H and resid 48:60)H48 - 60
6X-RAY DIFFRACTION6(chain H and resid 61:77)H61 - 77
7X-RAY DIFFRACTION7(chain H and resid 78:111)H78 - 111
8X-RAY DIFFRACTION8(chain H and resid 112:123)H112 - 123
9X-RAY DIFFRACTION9(chain H and resid 124:128)H124 - 128
10X-RAY DIFFRACTION10(chain H and resid 129:186)H129 - 186
11X-RAY DIFFRACTION11(chain H and resid 187:204)H187 - 204
12X-RAY DIFFRACTION12(chain H and resid 205:210)H205 - 210
13X-RAY DIFFRACTION13(chain L and resid 1:4)L1 - 4
14X-RAY DIFFRACTION14(chain L and resid 5:23)L5 - 23
15X-RAY DIFFRACTION15(chain L and resid 24:38)L24 - 38
16X-RAY DIFFRACTION16(chain L and resid 39:48)L39 - 48
17X-RAY DIFFRACTION17(chain L and resid 49:93)L49 - 93
18X-RAY DIFFRACTION18(chain L and resid 94:105)L94 - 105
19X-RAY DIFFRACTION19(chain L and resid 106:126)L106 - 126
20X-RAY DIFFRACTION20(chain L and resid 127:146)L127 - 146
21X-RAY DIFFRACTION21(chain L and resid 147:159)L147 - 159
22X-RAY DIFFRACTION22(chain L and resid 160:183)L160 - 183
23X-RAY DIFFRACTION23(chain L and resid 184:201)L184 - 201
24X-RAY DIFFRACTION24(chain L and resid 202:214)L202 - 214

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