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- PDB-3sge: Crystal structure of mAb 17.2 in complex with R13 peptide -

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Basic information

Entry
Database: PDB / ID: 3sge
TitleCrystal structure of mAb 17.2 in complex with R13 peptide
Components
  • Heavy Chain
  • Light Chain
  • R13 peptide
KeywordsIMMUNE SYSTEM / Immunoglobulin / Antigen binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsPizarro, J.C. / Boulot, G. / Hontebeyrie, M. / Bentley, G.A.
CitationJournal: Plos Negl Trop Dis / Year: 2011
Title: Crystal structure of the complex mAb 17.2 and the C-terminal region of Trypanosoma cruzi P2 Beta protein: implications in cross-reactivity
Authors: Pizarro, J.C. / Boulot, G. / Bentley, G.A. / Gomez, K.A. / Hoebeke, J. / Hontebeyrie, M. / Levin, M.J. / Smulski, C.R.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Light Chain
H: Heavy Chain
I: Light Chain
J: Heavy Chain
K: R13 peptide
M: R13 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5468
Polymers98,4666
Non-polymers802
Water13,295738
1
L: Light Chain
H: Heavy Chain
K: R13 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2734
Polymers49,2333
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-41 kcal/mol
Surface area20590 Å2
MethodPISA
2
I: Light Chain
J: Heavy Chain
M: R13 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2734
Polymers49,2333
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-40 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.000, 68.210, 92.120
Angle α, β, γ (deg.)90.00, 98.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light Chain


Mass: 24178.895 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Cell: HYBRIDOMA
#2: Antibody Heavy Chain


Mass: 23535.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/c / Cell: HYBRIDOMA
#3: Protein/peptide R13 peptide


Mass: 1518.513 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 738 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 18% (w/v) PEG 8000, 0.1M sodium cacodylate pH 6.7, 0.2M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 122 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.89→30 Å / Num. obs: 73894 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.47 % / Biso Wilson estimate: 31.21 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.9

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER2.9.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3SGD

3sgd


Resolution: 1.89→29.69 Å / Cor.coef. Fo:Fc: 0.9522 / Cor.coef. Fo:Fc free: 0.9397 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 3714 5.03 %RANDOM
Rwork0.1795 ---
obs0.1811 73894 90.5 %-
Displacement parametersBiso mean: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1-3.7762 Å20 Å21.4246 Å2
2---5.8871 Å20 Å2
3---2.1109 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: LAST / Resolution: 1.89→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6863 0 2 738 7603
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017053HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.159604HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2376SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes166HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1020HARMONIC5
X-RAY DIFFRACTIONt_it7053HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion18.14
X-RAY DIFFRACTIONt_chiral_improper_torsion944SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7906SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2459 134 4.92 %
Rwork0.2178 2592 -
all0.2191 2726 -
obs--90.5 %

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