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- PDB-1s3k: Crystal Structure of a Humanized Fab (hu3S193) in Complex with th... -

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Basic information

Entry
Database: PDB / ID: 1s3k
TitleCrystal Structure of a Humanized Fab (hu3S193) in Complex with the Lewis Y Tetrasaccharide
Components
  • HU3S193 Fab fragment, heavy chain
  • HU3S193 Fab fragment, light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Beta Barrel / Humanized antibody / Antigen binding fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Lewis Y antigen, alpha anomer
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRamsland, P.A. / Farrugia, W. / Bradford, T.M. / Hogarth, P.M. / Scott, A.M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structural convergence of antibody binding of carbohydrate determinants in lewis y tumor antigens
Authors: Ramsland, P.A. / Farrugia, W. / Bradford, T.M. / Hogarth, P.M. / Scott, A.M.
History
DepositionJan 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 1, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: chem_comp / entity_src_gen / struct_conn
Item: _chem_comp.type / _entity_src_gen.gene_src_common_name ..._chem_comp.type / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: HU3S193 Fab fragment, light chain
H: HU3S193 Fab fragment, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6314
Polymers47,8632
Non-polymers7682
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-9 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.758, 71.758, 90.142
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Antibody HU3S193 Fab fragment, light chain


Mass: 24066.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: murine complementarity determining regions grafted onto human framework and constant sequences
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Homo, Mus / Species: , / Strain: , / Description: Humanized / Cell (production host): NS0 murine myeloma cells / Production host: Mus musculus (house mouse)
#2: Antibody HU3S193 Fab fragment, heavy chain


Mass: 23796.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: murine complementarity determining regions grafted onto human framework and constant sequences
Source: (gene. exp.) Mus musculus (house mouse) / Genus: Mus, Homo / Species: , / Strain: , / Description: Humanized / Cell (production host): NS0 murine myeloma cells / Production host: Mus musculus (house mouse)
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis Y antigen / alpha anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis Y antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 20000, sodium chloride, Tris, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 39562 / Num. obs: 39562 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 15.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 3008 / Rsym value: 0.153 / % possible all: 73.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLY

1cly


Resolution: 1.9→33.34 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1950 -RANDOM
Rwork0.203 ---
obs0.203 38945 95.1 %-
all-38945 --
Displacement parametersBiso mean: 27.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 52 346 3679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.78

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