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- PDB-5owp: Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5owp
TitleCrystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3
Components
  • 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
  • Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / immune response / extracellular space
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 / Immunoglobulins ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Ig lambda-1 chain V region H2020 / Ig heavy chain V-III region J606
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsBermejo, I.A. / Albuquerque, I.S. / Somovilla, V.J. / Martinez-Saez, N. / Castro-Lopez, J. / Garcia-Martin, F. / Hinou, H. / Nishimura, S. / Jimenez-Barbero, J. / Asensio, J.L. ...Bermejo, I.A. / Albuquerque, I.S. / Somovilla, V.J. / Martinez-Saez, N. / Castro-Lopez, J. / Garcia-Martin, F. / Hinou, H. / Nishimura, S. / Jimenez-Barbero, J. / Asensio, J.L. / Avenoza, A. / Busto, J.H. / Hurtado-Guerrero, R. / Peregrina, J.M. / Bernardes, G.J. / Corzana, F.
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: The Use of Fluoroproline in MUC1 Antigen Enables Efficient Detection of Antibodies in Patients with Prostate Cancer.
Authors: Somovilla, V.J. / Bermejo, I.A. / Albuquerque, I.S. / Martinez-Saez, N. / Castro-Lopez, J. / Garcia-Martin, F. / Companon, I. / Hinou, H. / Nishimura, S.I. / Jimenez-Barbero, J. / Asensio, J. ...Authors: Somovilla, V.J. / Bermejo, I.A. / Albuquerque, I.S. / Martinez-Saez, N. / Castro-Lopez, J. / Garcia-Martin, F. / Companon, I. / Hinou, H. / Nishimura, S.I. / Jimenez-Barbero, J. / Asensio, J.L. / Avenoza, A. / Busto, J.H. / Hurtado-Guerrero, R. / Peregrina, J.M. / Bernardes, G.J.L. / Corzana, F.
History
DepositionSep 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
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_role
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: Ig heavy chain V-III region J606,Ig lambda-1 chain V region H2020
D: 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9996
Polymers26,5912
Non-polymers4074
Water2,576143
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint8 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.399, 68.151, 90.358
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 heavy chain V-III region J606,Ig lambda-1 chain V region H2020


Mass: 25758.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Komagataella pastoris (fungus) / References: UniProt: P01801, UniProt: P01726
#2: Protein/peptide 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE


Mass: 832.855 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.: 3 / 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.: 143 / 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: 1.98 Å3/Da / Density % sol: 37.77 %
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: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→90.36 Å / Num. obs: 19335 / % possible obs: 99.7 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rpim(I) all: 0.049 / Net I/σ(I): 10.9
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.685 / Rpim(I) all: 0.394 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5A2K

5a2k


Resolution: 1.85→90.36 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.488 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25614 561 2.9 %RANDOM
Rwork0.19428 ---
obs0.19599 18727 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.899 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2--0.64 Å20 Å2
3----2.23 Å2
Refinement stepCycle: 1 / Resolution: 1.85→90.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1777 0 26 143 1946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021842
X-RAY DIFFRACTIONr_bond_other_d0.0050.021675
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9632499
X-RAY DIFFRACTIONr_angle_other_deg1.2293.0123844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.81224.13375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22815268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.794158
X-RAY DIFFRACTIONr_chiral_restr0.1070.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212082
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02437
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_it1.5072.204904
X-RAY DIFFRACTIONr_mcbond_other1.5022.204904
X-RAY DIFFRACTIONr_mcangle_it2.4173.2831123
X-RAY DIFFRACTIONr_mcangle_other2.4183.2891124
X-RAY DIFFRACTIONr_scbond_it1.7912.687938
X-RAY DIFFRACTIONr_scbond_other1.792.688938
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8083.9111377
X-RAY DIFFRACTIONr_long_range_B_refined6.0628.5582050
X-RAY DIFFRACTIONr_long_range_B_other6.05928.5992051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 41 -
Rwork0.316 1344 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.1062 Å / Origin y: 1.5354 Å / Origin z: 12.8662 Å
111213212223313233
T0.2534 Å20.0015 Å2-0.0021 Å2-0.04 Å2-0.0112 Å2--0.0124 Å2
L0.1868 °2-0.1454 °20.0098 °2-0.6402 °20.5192 °2--0.5909 °2
S0.0342 Å °-0.0204 Å °-0.0053 Å °-0.0167 Å °0.0207 Å °-0.0643 Å °-0.0523 Å °-0.0411 Å °-0.0549 Å °

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