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- PDB-4hdi: Crystal Structure of 3E5 IgG3 FAB from mus musculus -

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Basic information

Entry
Database: PDB / ID: 4hdi
TitleCrystal Structure of 3E5 IgG3 FAB from mus musculus
Components
  • Ig heavy chain V region RF, Ig gamma-3 chain C region
  • Kappa light chain variable region, Anti-colorectal carcinoma light chain
KeywordsIMMUNE SYSTEM / IgG / FAB
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular region / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Ig heavy chain Mem5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsJanda, A. / Eryilmaz, E. / Kim, J. / Cordero, R.J.B. / Cowburn, D. / Casadevall, A.
CitationJournal: Mol.Immunol. / Year: 2013
Title: Global structures of IgG isotypes expressing identical variable regions.
Authors: Eryilmaz, E. / Janda, A. / Kim, J. / Cordero, R.J. / Cowburn, D. / Casadevall, A.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
L: Kappa light chain variable region, Anti-colorectal carcinoma light chain
H: Ig heavy chain V region RF, Ig gamma-3 chain C region
A: Kappa light chain variable region, Anti-colorectal carcinoma light chain
B: Ig heavy chain V region RF, Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)95,8634
Polymers95,8634
Non-polymers00
Water1,17165
1
L: Kappa light chain variable region, Anti-colorectal carcinoma light chain
H: Ig heavy chain V region RF, Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)47,9322
Polymers47,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-28 kcal/mol
Surface area19630 Å2
MethodPISA
2
A: Kappa light chain variable region, Anti-colorectal carcinoma light chain
B: Ig heavy chain V region RF, Ig gamma-3 chain C region


Theoretical massNumber of molelcules
Total (without water)47,9322
Polymers47,9322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-21 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.070, 98.289, 142.363
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 Kappa light chain variable region, Anti-colorectal carcinoma light chain


Mass: 24152.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IgG1 anti-TS1 VL, Gm16939 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A2NHM3*PLUS
#2: Antibody Ig heavy chain V region RF, Ig gamma-3 chain C region


Mass: 23778.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P84751*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.45 Å3/Da / Density % sol: 49.74 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 15, 2008
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.449→50 Å / Num. obs: 35380 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.8
Reflection shellResolution: 2.449→2.54 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
REFMAC5.7.0029refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H1P, 1T66
Resolution: 2.449→43.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 21.565 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.526 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26348 1770 5 %RANDOM
Rwork0.20841 ---
obs0.21134 33544 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.647 Å2
Baniso -1Baniso -2Baniso -3
1--5.46 Å20 Å20 Å2
2--5.02 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.449→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6677 0 0 65 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026842
X-RAY DIFFRACTIONr_bond_other_d0.0010.026285
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9549324
X-RAY DIFFRACTIONr_angle_other_deg0.7913.00214498
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1335871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44423.588262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1971534
X-RAY DIFFRACTIONr_chiral_restr0.0840.21065
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217733
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021549
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.449→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 107 -
Rwork0.307 2445 -
obs--98.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.3933-0.01262.15020.26050.30181.80570.3194-0.3126-0.28170.0727-0.1129-0.05150.4069-0.2975-0.20660.2903-0.0172-0.04760.08870.06850.11870.079119.040729.6315
23.89840.39962.00180.630.56991.2819-0.0246-0.13330.2998-0.0068-0.054-0.03020.0494-0.05790.07860.22980.03920.01070.0277-0.02990.06567.4135.412928.5834
31.86570.60280.48361.46240.58290.9654-0.0346-0.12890.30750.21340.0439-0.015-0.0499-0.1938-0.00930.23310.0396-0.04360.0706-0.02980.129515.621755.76025.5968
41.7033-0.0090.30420.74250.35130.8752-0.01960.23520.2481-0.01170.1549-0.19530.01010.0421-0.13540.19520.0123-0.0070.07450.00280.159525.369451.1234-8.8642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 219
2X-RAY DIFFRACTION2H1 - 220
3X-RAY DIFFRACTION3A1 - 217
4X-RAY DIFFRACTION4B2 - 220

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