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- PDB-1clo: ANTI-CARCINOEMBRYONIC ANTIGEN MONOCLONAL ANTIBODY A5B7 -

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Basic information

Entry
Database: PDB / ID: 1clo
TitleANTI-CARCINOEMBRYONIC ANTIGEN MONOCLONAL ANTIBODY A5B7
Components(A5B7 MONOCLONAL ANTIBODY) x 2
KeywordsIMMUNOGLOBULIN / FAB-FRAGMENT
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm
Similarity search - Function
: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBanfield, M.J. / King, D.J. / Mountain, A. / Brady, R.L.
Citation
Journal: 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.
#1: Journal: To be Published
Title: VL:VH Domain Rotations in Engineeded Antibodies: Crystal Structures of the Fab Fragments from Two Murine Anti-Tumour Antibodies and Their Engineered Human Constructs
Authors: Banfield, M.J. / King, D.J. / Mountain, A. / Brady, R.L.
History
DepositionMay 1, 1996Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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: A5B7 MONOCLONAL ANTIBODY
H: A5B7 MONOCLONAL ANTIBODY


Theoretical massNumber of molelcules
Total (without water)47,3062
Polymers47,3062
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-24 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.890, 79.680, 68.520
Angle α, β, γ (deg.)90.00, 104.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody A5B7 MONOCLONAL ANTIBODY


Mass: 23238.602 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT, FAB / Source method: isolated from a natural source
Details: ANTI-CARCINOEMBRYONIC ANTIGEN MONOCLONAL ANTIBODY A5B7
Source: (natural) Mus musculus (house mouse) / References: GenBank: 1042224
#2: Antibody A5B7 MONOCLONAL ANTIBODY


Mass: 24067.021 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT, FAB / Source method: isolated from a natural source
Details: ANTI-CARCINOEMBRYONIC ANTIGEN MONOCLONAL ANTIBODY A5B7
Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FAB FRAGMENT IS NUMBERED ACCORDING TO THE KABAT SYSTEM (E.A.KABAT, T.T.WU,M.REID-MILLER,H.M. ...THE FAB FRAGMENT IS NUMBERED ACCORDING TO THE KABAT SYSTEM (E.A.KABAT, T.T.WU,M.REID-MILLER,H.M.PERRY, K.S.GOTTESMAN (1987) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD).

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop / Details: Banfield, M.J., (1996) Acta Cryst. D., 52, 1107.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMBis-Tris1drop
317-21 %PEG40001reservoir
450 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 27439 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 24.1
Reflection shellResolution: 2→2.15 Å / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 9.7 / % possible all: 98
Reflection
*PLUS
Num. measured all: 95102
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→8 Å / σ(F): 0
Details: WEAK ELECTRON DENSITY ONLY IS PRESENT FOR RESIDUES L 155 - L 159 AND H 130 - H 134.
RfactorNum. reflection% reflection
Rwork0.212 --
obs0.212 23098 99.5 %
Displacement parametersBiso mean: 23.67 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 0 400 3727
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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