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- PDB-3i75: Antibody Structure -

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Basic information

Entry
Database: PDB / ID: 3i75
TitleAntibody Structure
Components
  • Antibody heavy chainImmunoglobulin heavy chain
  • Antibody light chainImmunoglobulin light chain
KeywordsIMMUNE SYSTEM / Antibody / IgG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsIsaacs, N.W. / Riboldi-Tunnicliffe, A.
CitationJournal: To be Published
Title: Antibody Structure
Authors: Riboldi-Tunnicliffe, A. / Isaacs, N.W.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Antibody heavy chain
B: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,37211
Polymers47,5762
Non-polymers7969
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-26 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.662, 129.662, 74.505
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-229-

SO4

21B-308-

HOH

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody Antibody heavy chain / Immunoglobulin heavy chain


Mass: 23449.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Antibody light chain / Immunoglobulin light chain


Mass: 24125.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 4 types, 261 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHOR DID NOT PROVIDE EXACT SEQUENCE FOR RESIDUES 140 AND 141 IN CHAIN B.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jun 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→111 Å / Num. obs: 51886

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIM

1mim


Resolution: 1.95→64.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.791 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 2571 5.1 %RANDOM
Rwork0.17966 ---
obs0.18139 47927 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.778 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→64.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 43 252 3628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0213475
X-RAY DIFFRACTIONr_bond_other_d0.0020.022981
X-RAY DIFFRACTIONr_angle_refined_deg2.1691.964733
X-RAY DIFFRACTIONr_angle_other_deg1.12337002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2375432
X-RAY DIFFRACTIONr_chiral_restr0.1390.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023807
X-RAY DIFFRACTIONr_gen_planes_other0.010.02679
X-RAY DIFFRACTIONr_nbd_refined0.2070.2461
X-RAY DIFFRACTIONr_nbd_other0.2650.23311
X-RAY DIFFRACTIONr_nbtor_other0.0920.22094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.213
X-RAY DIFFRACTIONr_mcbond_it1.8371.52165
X-RAY DIFFRACTIONr_mcangle_it3.00123520
X-RAY DIFFRACTIONr_scbond_it3.94931310
X-RAY DIFFRACTIONr_scangle_it6.0674.51213
X-RAY DIFFRACTIONr_rigid_bond_restr2.41123475
X-RAY DIFFRACTIONr_sphericity_free7.1162253
X-RAY DIFFRACTIONr_sphericity_bonded3.36623395
LS refinement shellResolution: 1.954→2.005 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 185
Rwork0.329 3238

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