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- PDB-5a2j: Crystal structure of scFv-SM3 in complex with the naked peptide APDTRP -

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Basic information

Entry
Database: PDB / ID: 5a2j
TitleCrystal structure of scFv-SM3 in complex with the naked peptide APDTRP
Components
  • SCFV-SM3
  • THE NAKED PEPTIDE APDTRP
KeywordsPEPTIDE BINDING PROTEIN / 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
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: 1.65 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 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: SCFV-SM3
P: THE NAKED PEPTIDE APDTRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6476
Polymers26,3992
Non-polymers2484
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint3.8 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.853, 35.486, 69.518
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody SCFV-SM3


Mass: 25742.338 Da / Num. of mol.: 1 / Fragment: RESIDUES 6-115,20-129
Source method: isolated from a genetically manipulated source
Details: CONTAINS BOTH H AND L CHAINS OF SCFV-SM3, CONNECTEDBY A LINKER. CHAIN L RESIDUES ARE NUMBERED FROM 1000.
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PPICZALPHAA / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P01801, UniProt: P01727
#2: Protein/peptide THE NAKED PEPTIDE APDTRP


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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.11 Å3/Da / Density % sol: 41.84 % / 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: 1.65→20 Å / Num. obs: 26087 / % possible obs: 97.1 % / Observed criterion σ(I): 1.98 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4 / % possible all: 95.8

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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: 1.65→68.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.23 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19733 756 2.9 %RANDOM
Rwork0.16643 ---
obs0.16737 25321 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20.56 Å2
2---0.18 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.65→68.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 16 207 1980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021829
X-RAY DIFFRACTIONr_bond_other_d0.0040.021681
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.932472
X-RAY DIFFRACTIONr_angle_other_deg0.8233855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28523.97478
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60115278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.281159
X-RAY DIFFRACTIONr_chiral_restr0.2270.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
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_it0.8141.088920
X-RAY DIFFRACTIONr_mcbond_other0.8141.087919
X-RAY DIFFRACTIONr_mcangle_it1.3831.6221128
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1771.225909
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: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 48 -
Rwork0.189 1852 -
obs--95.38 %
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)
10.2797-0.3058-0.06010.4109-0.12691.01350.0173-0.02310.0286-0.00450.0143-0.00880.07050.0423-0.03150.0289-0.0030.010.0045-0.00410.01312.66920.319825.8239
20.72710.2313-0.39080.2832-0.0470.3897-0.0022-0.01810.01020.00430.0037-0.03380.0001-0.0245-0.00150.0013-0.0002-0.00210.0124-0.00210.023612.3562-1.26416.2367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 112
2X-RAY DIFFRACTION2H1003 - 1107

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