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- PDB-1ae6: IGG-FAB FRAGMENT OF MOUSE MONOCLONAL ANTIBODY CTM01 -

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Basic information

Entry
Database: PDB / ID: 1ae6
TitleIGG-FAB FRAGMENT OF MOUSE MONOCLONAL ANTIBODY CTM01
Components
  • IGG CTM01 FAB (HEAVY CHAIN)
  • IGG CTM01 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / FAB FRAGMENT / HUMANISATION
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Ig gamma-1 chain C region, membrane-bound form / : / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBanfield, M.J. / Brady, R.L.
CitationJournal: Proteins / Year: 1997
Title: VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs.
Authors: Banfield, M.J. / King, D.J. / Mountain, A. / Brady, R.L.
History
DepositionMar 6, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG CTM01 FAB (LIGHT CHAIN)
H: IGG CTM01 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,6642
Polymers47,6642
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-24 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.300, 66.550, 61.350
Angle α, β, γ (deg.)90.00, 103.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IGG CTM01 FAB (LIGHT CHAIN)


Mass: 24194.924 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source
Details: EACH OF THE FOUR DOMAINS ADOPT THE IMMUNOGLOBULIN SUPERFAMILY FOLD
Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8VCI6
#2: Antibody IGG CTM01 FAB (HEAVY CHAIN)


Mass: 23469.332 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source
Details: EACH OF THE FOUR DOMAINS ADOPT THE IMMUNOGLOBULIN SUPERFAMILY FOLD
Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869, UniProt: Q99LC4*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 37.5 %
Crystal growpH: 5.6
Details: 20-25% PEG4000, BUFFERED AT PH 5.6 WITH 20MM BIS-TRIS.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMbis-Tris1drop
210 mg/mlprotein1drop
320-25 %PEG40001reservoir
420 mMBis-Tris1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 7862 / % possible obs: 91.1 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 40.8 Å2 / Rsym value: 0.138 / Net I/σ(I): 5
Reflection shellResolution: 3→3.23 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.252 / % possible all: 88.3
Reflection
*PLUS
Num. measured all: 15707 / Rmerge(I) obs: 0.138
Reflection shell
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AD9 - STRUCTURE OF THE ENGINEERED HUMAN CONSTRUCT OF CTM01

1ad9


Resolution: 3→15 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED ELECTRON DENSITY IS WEAK FOR RESIDUES H 96 - H 100A OF THE H3 HYPERVARIABLE LOOP. ALL ATOMS FOR THIS LOOP ARE INCLUDED IN THE FINAL MODEL, BUT THE DENSITY ONLY ...Details: BULK SOLVENT MODEL USED ELECTRON DENSITY IS WEAK FOR RESIDUES H 96 - H 100A OF THE H3 HYPERVARIABLE LOOP. ALL ATOMS FOR THIS LOOP ARE INCLUDED IN THE FINAL MODEL, BUT THE DENSITY ONLY ACCOUNTS FOR THE C-ALPHA TRACE.
RfactorNum. reflection% reflectionSelection details
Rfree0.311 538 6.9 %RANDOM
Rwork0.21 ---
obs0.21 7819 91.2 %-
Displacement parametersBiso mean: 44.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.33 Å
Luzzati d res low-10 Å
Luzzati sigma a0.64 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 0 3346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.14 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.461 58 6.3 %
Rwork0.338 862 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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