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- PDB-6frj: Crystal structure of scFv-SM3 in complex with APD-SeThrGalNAc-RP -

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Basic information

Entry
Database: PDB / ID: 6frj
TitleCrystal structure of scFv-SM3 in complex with APD-SeThrGalNAc-RP
Components
  • APD-SeThr-RP
  • scFv-SM3
KeywordsIMMUNE SYSTEM / Glycopeptides / antibodies / molecular recognition / conformation analysis
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2-acetamido-2-deoxy-alpha-D-galactopyranose
Function and homology information
Biological speciesMus musculus (house mouse)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCompanon, I. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Bernardes, G.J. / Boutureira, O. / Jimenez-Oses, G. ...Companon, I. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Bernardes, G.J. / Boutureira, O. / Jimenez-Oses, G. / Asensio, J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, F.
Funding support Spain, 2items
OrganizationGrant numberCountry
MICINNCTQ2013-44367-C2-2-P Spain
MICINNBFU2016-75633-P Spain
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage.
Authors: Companon, I. / Guerreiro, A. / Mangini, V. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / ...Authors: Companon, I. / Guerreiro, A. / Mangini, V. / Castro-Lopez, J. / Escudero-Casao, M. / Avenoza, A. / Busto, J.H. / Castillon, S. / Jimenez-Barbero, J. / Asensio, J.L. / Jimenez-Oses, G. / Boutureira, O. / Peregrina, J.M. / Hurtado-Guerrero, R. / Fiammengo, R. / Bernardes, G.J.L. / Corzana, F.
History
DepositionFeb 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn
Revision 1.2Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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
H: scFv-SM3
B: APD-SeThr-RP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9457
Polymers26,4762
Non-polymers4695
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The molecule is monomeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint11 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.353, 68.612, 90.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody scFv-SM3


Mass: 25758.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Although this structure is a ScFv, please follow the same numbering as shown in PDB entry 5OWP.
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus)
#2: Protein/peptide APD-SeThr-RP


Mass: 717.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 disodium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→54.7 Å / Num. obs: 41360 / % possible obs: 93.4 % / Redundancy: 5.3 % / CC1/2: 0.996 / Rpim(I) all: 0.031 / Net I/σ(I): 12
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.3 / CC1/2: 0.892 / Rpim(I) all: 0.327 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SM3

1sm3


Resolution: 1.4→54.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.345 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22968 1617 3.9 %RANDOM
Rwork0.2048 ---
obs0.20578 39679 93.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.356 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--1.65 Å20 Å2
3----1.9 Å2
Refinement stepCycle: 1 / Resolution: 1.4→54.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 16 163 1959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021838
X-RAY DIFFRACTIONr_bond_other_d0.0040.021628
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9592496
X-RAY DIFFRACTIONr_angle_other_deg1.1053.0153773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24524.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.867158
X-RAY DIFFRACTIONr_chiral_restr0.0750.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0672.282906
X-RAY DIFFRACTIONr_mcbond_other1.0672.281904
X-RAY DIFFRACTIONr_mcangle_it1.8563.4171126
X-RAY DIFFRACTIONr_mcangle_other1.8553.4171126
X-RAY DIFFRACTIONr_scbond_it1.2832.571932
X-RAY DIFFRACTIONr_scbond_other1.2832.571932
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1213.7651370
X-RAY DIFFRACTIONr_long_range_B_refined4.15127.6191980
X-RAY DIFFRACTIONr_long_range_B_other4.1527.6561981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 125 -
Rwork0.301 3076 -
obs--99.88 %

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