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- PDB-1nbv: AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-D... -

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Basic information

Entry
Database: PDB / ID: 1nbv
TitleAN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX
Components
  • IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN)
  • IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / 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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / positive regulation of immune response / extracellular space / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
: / If kappa light chain / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHerron, J.N. / He, X.M. / Edmundson, A.B.
Citation
Journal: Proteins / Year: 1991
Title: An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.
Authors: Herron, J.N. / He, X.M. / Ballard, D.W. / Blier, P.R. / Pace, P.E. / Bothwell, A.L. / Voss Jr., E.W. / Edmundson, A.B.
#1: Journal: Mol.Immunol. / Year: 1985
Title: Crystallographic Characterization of the Fab Fragment of a Monoclonal Anti-Ss-DNA Antibody
Authors: Gibson, A.L. / Herron, J.N. / Ballard, D.W. / Voss, E.W. / He, X.M. / Patrick, V.A. / Edmundson, A.B.
History
DepositionMar 16, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Nov 20, 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: IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN)
H: IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,6632
Polymers47,6632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-28 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.400, 43.700, 41.500
Angle α, β, γ (deg.)83.40, 89.40, 84.40
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES PRO L 8, PRO L 100, PRO L 146, PRO H 155, AND PRO H 197 ARE CIS PROLINES.

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Components

#1: Antibody IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN)


Mass: 24109.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: S16112, UniProt: A2NHM3*PLUS
#2: Antibody IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN)


Mass: 23553.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P01867
Has protein modificationY
Sequence detailsTHE PROTEIN WAS SEQUENCED BY D.W. BALLARD, P.R. BLIER, P.E. PACE, AND A.L.M. BOTHWELL, REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.6 / Method: unknown
Components of the solutions
*PLUS
Conc.: 1.7 M / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 19716 / % possible obs: 72 % / Observed criterion σ(I): 2

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→6 Å /
RfactorNum. reflection
Rwork0.246 -
obs0.246 18797
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 0 0 3347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg
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
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 18797 / Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.025
X-RAY DIFFRACTIONx_angle_d0.030.032
X-RAY DIFFRACTIONx_planar_d0.030.026
X-RAY DIFFRACTIONx_plane_restr0.0250.014
X-RAY DIFFRACTIONx_chiral_restr0.150.179

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