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- PDB-6s2i: Anti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3 -

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Basic information

Entry
Database: PDB / ID: 6s2i
TitleAnti-tumor antibody 14F7-derived scFv in complex with NeuGc Gm3
ComponentsscFv C1
KeywordsANTITUMOR PROTEIN / ganglioside / complex / scfv / antibody fragment / single chain fragment variable / immuno therapy / 14F7 / gm3
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.285 Å
AuthorsBjerregaard-Andersen, K. / Heggelund, J.E. / Krengel, U.
CitationJournal: Glycobiology / Year: 2021
Title: Key role of a structural water molecule for the specificity of 14F7-An antitumor antibody targeting the NeuGc GM3 ganglioside.
Authors: Bjerregaard-Andersen, K. / Abraha, F. / Johannesen, H. / Oscarson, S. / Moreno, E. / Krengel, U.
History
DepositionJun 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 2.0Feb 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value
Revision 2.1Jan 26, 2022Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_entity_branch_descriptor
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: scFv C1
B: scFv C1
C: scFv C1
D: scFv C1
E: scFv C1
F: scFv C1
G: scFv C1
H: scFv C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,5799
Polymers224,9308
Non-polymers6501
Water1,874104
1
A: scFv C1
B: scFv C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8823
Polymers56,2322
Non-polymers6501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-11 kcal/mol
Surface area11060 Å2
MethodPISA
2
C: scFv C1
D: scFv C1


Theoretical massNumber of molelcules
Total (without water)56,2322
Polymers56,2322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-8 kcal/mol
Surface area11480 Å2
MethodPISA
3
E: scFv C1
F: scFv C1


Theoretical massNumber of molelcules
Total (without water)56,2322
Polymers56,2322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area10970 Å2
MethodPISA
4
G: scFv C1
H: scFv C1


Theoretical massNumber of molelcules
Total (without water)56,2322
Polymers56,2322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-11 kcal/mol
Surface area11110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 113.690, 66.950
Angle α, β, γ (deg.)90.00, 91.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
scFv C1


Mass: 28116.238 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide N-glycolyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 649.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Gca2-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCCO/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Gc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.33 Å3/Da / Density % sol: 47.11 % / Description: Plates
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3- ...Details: 12.5 % w/v PEG 1000, 12.5 % w/v PEG 3350, 12.5 % v/v MPD, 0.02 M 1,6-hexandiol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M bicine/tris base pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.285→62.9 Å / Num. obs: 42116 / % possible obs: 98.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 44.029 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.053 / Rrim(I) all: 0.111 / Net I/σ(I): 9.03
Reflection shellResolution: 2.285→2.325 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2141 / CC1/2: 0.813 / Rpim(I) all: 0.379 / Rrim(I) all: 0.795 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FFJ

6ffj


Resolution: 2.285→62.865 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.43
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 2151 5.11 %Random
Rwork0.2219 ---
obs0.2237 42066 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.46 Å2
Refinement stepCycle: LAST / Resolution: 2.285→62.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7239 0 44 104 7387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027473
X-RAY DIFFRACTIONf_angle_d0.54210155
X-RAY DIFFRACTIONf_dihedral_angle_d10.9414423
X-RAY DIFFRACTIONf_chiral_restr0.0411104
X-RAY DIFFRACTIONf_plane_restr0.0041289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2853-2.33840.42791260.39312675X-RAY DIFFRACTION99
2.3384-2.39690.42021400.37352668X-RAY DIFFRACTION99
2.3969-2.46170.40131280.34952667X-RAY DIFFRACTION99
2.4617-2.53410.42841350.32692661X-RAY DIFFRACTION99
2.5341-2.61590.36421370.30942674X-RAY DIFFRACTION99
2.6159-2.70940.36021490.28392654X-RAY DIFFRACTION99
2.7094-2.81790.28081350.27072690X-RAY DIFFRACTION99
2.8179-2.94620.35191430.27142641X-RAY DIFFRACTION99
2.9462-3.10150.26941260.23622697X-RAY DIFFRACTION99
3.1015-3.29580.27861580.21852656X-RAY DIFFRACTION99
3.2958-3.55030.22631330.19632675X-RAY DIFFRACTION99
3.5503-3.90750.21011710.18922443X-RAY DIFFRACTION92
3.9075-4.47280.17781370.15892724X-RAY DIFFRACTION100
4.4728-5.63470.18891480.16032702X-RAY DIFFRACTION100
5.6347-62.88910.21341850.19262688X-RAY DIFFRACTION99

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