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- PDB-1bog: ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-HOMO... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1bog
TitleANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-HOMOLOGOUS PEPTIDE
Components
  • (ANTIBODY (CB 4-1)) x 2
  • PEPTIDE
KeywordsCOMPLEX (ANTIBODY/PEPTIDE) / POLYSPECIFICITY / CROSS REACTIVITY / FAB-FRAGMENT / HIV-1 / COMPLEX (ANTIBODY-PEPTIDE) / COMPLEX (ANTIBODY-PEPTIDE) complex
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
Similarity search - Function
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/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
: / Ig gamma-2A chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKeitel, T. / Kramer, A. / Wessner, H. / Scholz, C. / Schneider-Mergener, J. / Hoehne, W.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity.
Authors: Keitel, T. / Kramer, A. / Wessner, H. / Scholz, C. / Schneider-Mergener, J. / Hohne, W.
History
DepositionAug 4, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY (CB 4-1)
B: ANTIBODY (CB 4-1)
C: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)47,8293
Polymers47,8293
Non-polymers00
Water86548
1
A: ANTIBODY (CB 4-1)
B: ANTIBODY (CB 4-1)
C: PEPTIDE

A: ANTIBODY (CB 4-1)
B: ANTIBODY (CB 4-1)
C: PEPTIDE


Theoretical massNumber of molelcules
Total (without water)95,6576
Polymers95,6576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Unit cell
Length a, b, c (Å)104.430, 104.430, 295.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody ANTIBODY (CB 4-1)


Mass: 23972.771 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: FAB DERIVED FROM IGG2A KAPPA / Source: (natural) Mus musculus (house mouse) / Cell line: CB 4-1-1-F6 B-CELL HYBRIDOMA / Strain: BALB-C / References: GenBank: 387371
#2: Antibody ANTIBODY (CB 4-1)


Mass: 22669.508 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: FAB DERIVED FROM IGG2A KAPPA / Source: (natural) Mus musculus (house mouse) / Cell line: CB 4/1/1/F6 B-CELL HYBRIDOMA / Strain: BALB/C / References: UniProt: P01864
#3: Protein/peptide PEPTIDE /


Mass: 1186.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 4.8 Å3/Da / Density % sol: 71 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlFab1drop
21.8 Mammonium sulfate1reservoir
30.1 M2-(N-morpholino)-propanesulfonic acid1reservoir
40.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: BENT MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.6→91 Å / Num. obs: 30270 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
REFMACrefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HFL

2hfl
PDB Unreleased entry


Resolution: 2.6→91 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1540 5 %RANDOM
Rwork0.246 ---
obs-28360 96 %-
Refinement stepCycle: LAST / Resolution: 2.6→91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 0 48 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5682
X-RAY DIFFRACTIONp_mcangle_it2.7453
X-RAY DIFFRACTIONp_scbond_it1.8362
X-RAY DIFFRACTIONp_scangle_it2.9953
X-RAY DIFFRACTIONp_plane_restr0.02360.03
X-RAY DIFFRACTIONp_chiral_restr0.7820.15
X-RAY DIFFRACTIONp_singtor_nbd0.1950.3
X-RAY DIFFRACTIONp_multtor_nbd0.2510.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1960.3
X-RAY DIFFRACTIONp_planar_tor97
X-RAY DIFFRACTIONp_staggered_tor23.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.120
X-RAY DIFFRACTIONp_special_tor83.915
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS

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