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- PDB-6ug9: Complex of ch28/11 Fab and SSEA-4 (hexagonal form) -

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Basic information

Entry
Database: PDB / ID: 6ug9
TitleComplex of ch28/11 Fab and SSEA-4 (hexagonal form)
Components
  • ch28/11 Fab heavy chain
  • ch28/11 Fab light chain
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / CHIMERIC ANTIBODY / ANTIGEN BINDING FRAGMENT / SSEA-4 / COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsSoliman, C. / Ramsland, P.A.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The terminal sialic acid of stage-specific embryonic antigen-4 has a crucial role in binding to a cancer-targeting antibody.
Authors: Soliman, C. / Chua, J.X. / Vankemmelbeke, M. / McIntosh, R.S. / Guy, A.J. / Spendlove, I. / Durrant, L.G. / Ramsland, P.A.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.value
Revision 1.2Jan 1, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Category: chem_comp / citation
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
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 / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ch28/11 Fab light chain
H: ch28/11 Fab heavy chain
B: ch28/11 Fab light chain
A: ch28/11 Fab heavy chain
K: ch28/11 Fab light chain
J: ch28/11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0349
Polymers138,5516
Non-polymers3,4833
Water2,378132
1
L: ch28/11 Fab light chain
H: ch28/11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3453
Polymers46,1842
Non-polymers1,1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-5 kcal/mol
Surface area19150 Å2
MethodPISA
2
B: ch28/11 Fab light chain
A: ch28/11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3453
Polymers46,1842
Non-polymers1,1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-4 kcal/mol
Surface area19130 Å2
MethodPISA
3
K: ch28/11 Fab light chain
J: ch28/11 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3453
Polymers46,1842
Non-polymers1,1611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-5 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.952, 169.952, 95.435
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Antibody ch28/11 Fab light chain


Mass: 23166.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody ch28/11 Fab heavy chain


Mass: 23016.844 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1161.026 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-3DGalpa1-4DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4-2-5/a4-b1_b4-c1_c3-d1_d3-e1_e3-f2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(4+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 4000, iso-Propanol, sodium HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.74→50 Å / Num. obs: 41405 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rrim(I) all: 0.14 / Net I/σ(I): 10.6
Reflection shellResolution: 2.74→2.8 Å / Num. unique obs: 6561 / Rrim(I) all: 0.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UG7

6ug7


Resolution: 2.74→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.346
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2469 1992 4.8 %RANDOM
Rwork0.1699 ---
obs0.1735 41356 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.91 Å2 / Biso mean: 54.8146 Å2 / Biso min: 18.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.47 Å20 Å2
2--0.94 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.74→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9596 0 237 132 9965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0210088
X-RAY DIFFRACTIONr_bond_other_d00.029203
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.97713744
X-RAY DIFFRACTIONr_angle_other_deg3.824321395
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.60351264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21424.538357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.428151569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3511527
X-RAY DIFFRACTIONr_chiral_restr0.0880.21606
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111101
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022170
X-RAY DIFFRACTIONr_mcbond_it3.3915.3015083
X-RAY DIFFRACTIONr_mcbond_other3.3895.35082
X-RAY DIFFRACTIONr_mcangle_it5.2677.9436338
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 147 -
Rwork0.325 2870 -
all-3017 -
obs--99.64 %

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