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- PDB-3if1: Crystal structure of 237mAb in complex with a GalNAc -

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Basic information

Entry
Database: PDB / ID: 3if1
TitleCrystal structure of 237mAb in complex with a GalNAc
Components(Immunoglobulin ...Antibody) x 2
KeywordsIMMUNE SYSTEM / glycopepitde / antibody / Fab / carbohydrate-biding / tumour
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2-acetamido-2-deoxy-beta-D-galactopyranose
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsBrooks, C.L. / Evans, S.V. / Borisova, S.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Antibody recognition of a unique tumor-specific glycopeptide antigen.
Authors: Brooks, C.L. / Schietinger, A. / Borisova, S.N. / Kufer, P. / Okon, M. / Hirama, T. / Mackenzie, C.R. / Wang, L.X. / Schreiber, H. / Evans, S.V.
#1: Journal: Science / Year: 2006
Title: A mutant chaperone converts a wild-type protein into a tumor-specific antigen
Authors: Schietinger, A. / Philip, M. / Yoshida, B.A. / Azadi, P. / Liu, H. / Meredith, S.C. / Schreiber, H.
History
DepositionJul 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin light chain (IgG2a)
B: Immunoglobulin heavy chain (IgG2a)
C: Immunoglobulin light chain (IgG2a)
D: Immunoglobulin heavy chain (IgG2a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,89216
Polymers94,0014
Non-polymers89112
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Immunoglobulin light chain (IgG2a)
B: Immunoglobulin heavy chain (IgG2a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4668
Polymers47,0002
Non-polymers4666
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-25 kcal/mol
Surface area19170 Å2
MethodPISA
3
C: Immunoglobulin light chain (IgG2a)
D: Immunoglobulin heavy chain (IgG2a)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4258
Polymers47,0002
Non-polymers4256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-25 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)279.350, 38.420, 95.990
Angle α, β, γ (deg.)90.000, 109.110, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Immunoglobulin light chain (IgG2a)


Mass: 23591.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Production host: Mus musculus (house mouse)
#2: Antibody Immunoglobulin heavy chain (IgG2a)


Mass: 23409.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Production host: Mus musculus (house mouse)

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Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE / N-Acetylgalactosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-galactopyranosamineCOMMON NAMEGMML 1.0
b-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 433 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5000, ZnCl2, MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2007 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→19.93 Å / Num. obs: 38606 / % possible obs: 99 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.073 / Χ2: 0.85 / Net I/σ(I): 8.4 / Scaling rejects: 2071
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.39-2.483.340.2713.31265737531.198.5
2.48-2.573.320.2363.61285538311.0198.6
2.57-2.693.330.2014.21274637841.0698.9
2.69-2.833.380.1595.11303438170.9498.9
2.83-3.013.40.1255.91333038650.8799.5
3.01-3.243.480.0957.81367938870.8199.8
3.24-3.573.50.0719.91374238580.7399.5
3.57-4.083.520.05812.41389538760.6999.3
4.08-5.123.520.04615.71406338940.6598.5
5.12-19.933.360.04615.11392640410.6898.7

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IET
Resolution: 2.39→19.93 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.08 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.285 1938 5.02 %
Rwork0.224 --
obs0.228 38592 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.114 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso max: 84.43 Å2 / Biso mean: 31.035 Å2 / Biso min: 5.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.331 Å20 Å20.349 Å2
2--1.642 Å20 Å2
3----1.973 Å2
Refinement stepCycle: LAST / Resolution: 2.39→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 40 423 6981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046708
X-RAY DIFFRACTIONf_angle_d0.8469104
X-RAY DIFFRACTIONf_chiral_restr0.0571026
X-RAY DIFFRACTIONf_plane_restr0.0031158
X-RAY DIFFRACTIONf_dihedral_angle_d17.6832380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.39-2.450.3441320.2382529266198
2.45-2.5160.331460.2472579272598
2.516-2.5890.3441340.2522619275399
2.589-2.6730.3361250.2482573269899
2.673-2.7680.3261330.2562588272199
2.768-2.8790.3571390.2412593273299
2.879-3.0090.3031160.2482638275499
3.009-3.1670.2951460.23426142760100
3.167-3.3650.2771440.20726192763100
3.365-3.6230.2561420.1926362778100
3.623-3.9850.2361310.1962638276999
3.985-4.5560.2081290.1732647277699
4.556-5.7170.2631550.1862648280399
5.717-19.9350.2831660.2592733289998

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