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- PDB-5a2k: Crystal structure of scFv-SM3 in complex with APD-TGalNAc-RP -

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Basic information

Entry
Database: PDB / ID: 5a2k
TitleCrystal structure of scFv-SM3 in complex with APD-TGalNAc-RP
Components
  • ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC
  • IG LAMBDA-1 CHAIN V REGION S43
KeywordsIMMUNE SYSTEM / GLYCOPEPTIDES / ANTIBODIES / MOLECULAR RECOGNITION / CONFORMATION ANALYSIS / FUSION PROTEIN
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular region
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Ig lambda-1 chain V region S43 / Ig heavy chain V-III region J606
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMartinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. ...Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, F.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Deciphering the Non-Equivalence of Serine and Threonine O-Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an Anti-Muc1 Antibody.
Authors: Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / ...Authors: Martinez-Saez, N. / Castro-Lopez, J. / Valero-Gonzalez, J. / Madariaga, D. / Companon, I. / Somovilla, V.J. / Salvado, M. / Asensio, J.L. / Jimenez-Barbero, J. / Avenoza, A. / Busto, J.H. / Bernardes, G.J.L. / Peregrina, J.M. / Hurtado-Guerrero, R. / Corzana, F.
History
DepositionMay 20, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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
Revision 2.2Nov 13, 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
H: IG LAMBDA-1 CHAIN V REGION S43
P: ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9939
Polymers26,3992
Non-polymers5947
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-3.7 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.418, 68.796, 90.414
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 IG LAMBDA-1 CHAIN V REGION S43 / SCFV-SM3


Mass: 25742.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-115,20-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P01801, UniProt: P01727
#2: Protein/peptide ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC


Mass: 656.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / 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.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L OF PDB ENTRY 1SM3 CHAIN P REPRESENTS A SHORTER ...RESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L OF PDB ENTRY 1SM3 CHAIN P REPRESENTS A SHORTER VERISON OF THE PEPTIDE PRESENT IN PDB ENTRY 1SM3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.01 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 25092 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SM3

1sm3


Resolution: 1.7→90.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.693 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21619 736 2.9 %RANDOM
Rwork0.17583 ---
obs0.17695 24300 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--1.46 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 1.7→90.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 38 188 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021833
X-RAY DIFFRACTIONr_bond_other_d0.0010.021692
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9432467
X-RAY DIFFRACTIONr_angle_other_deg0.81333875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29723.94776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78615274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.376159
X-RAY DIFFRACTIONr_chiral_restr0.0950.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022013
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
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_it1.4821.982914
X-RAY DIFFRACTIONr_mcbond_other1.4821.98913
X-RAY DIFFRACTIONr_mcangle_it2.4182.9511119
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.942.312919
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 61 -
Rwork0.235 1734 -
obs--99.94 %
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)
10.43950.3924-0.40910.7670.17021.32820.03250.02230.04230.03230.0882-0.0473-0.0265-0.036-0.12070.00730.00280.00090.0524-0.02240.024611.90517.664921.0174
20.36-0.1376-0.0550.79910.29840.42950.01890.0084-0.04670.0158-0.0243-0.0022-0.0827-0.00790.00550.02640.0015-0.00520.0336-0.00720.012310.545-5.46213.7481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 112
2X-RAY DIFFRACTION2H1003 - 1107

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