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

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Basic information

Entry
Database: PDB / ID: 1cfs
TitleANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-UNRELATED PEPTIDE
Components
  • PROTEIN (ANTIGEN BOUND PEPTIDE)
  • PROTEIN (IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN))
  • PROTEIN (IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN))
KeywordsPOLYSPECIFICITY / CROSS REACTIVITY / FAB-FRAGMENT / HIV-1
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / extracellular region / plasma membrane
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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Ig gamma-2A chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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
DepositionMar 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 31, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN))
B: PROTEIN (IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN))
C: PROTEIN (ANTIGEN BOUND PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)47,8223
Polymers47,8223
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-36 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.320, 85.320, 136.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody PROTEIN (IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN))


Mass: 23928.721 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: CB 4/1/1/F6 B-CELL HYBRIDOMA / Strain: BALB/C / References: UniProt: P01837*PLUS
#2: Antibody PROTEIN (IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN))


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


Mass: 1223.359 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 6.5
Details: 15% POLYETHYLENE GLYCOL 4000, 0.1 M (NH4)2SO4, 0.2% ETHANOL, pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlFab1drop
215 %PEG40001reservoir
30.1 Mammonium sulfate1reservoir
40.2 %ethanol1reservoir
50.1 MMES/NaOH1reservoir
60.02 %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: Nov 1, 1996 / Details: BENT MIRROR
RadiationMonochromator: GE(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.75→72 Å / Num. obs: 13769 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.062
Reflection shellHighest resolution: 2.75 Å / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
DENZOdata reduction
CCP4data reduction
AMoREphasing
CCP4refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→72 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.332 1509 11 %RANDOM
Rwork0.232 ---
all-12901 --
obs-28360 100 %-
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.75→72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 0 28 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.492
X-RAY DIFFRACTIONp_mcangle_it2.6263
X-RAY DIFFRACTIONp_scbond_it1.1782
X-RAY DIFFRACTIONp_scangle_it2.0723
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.780.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2080.3
X-RAY DIFFRACTIONp_planar_tor8.97
X-RAY DIFFRACTIONp_staggered_tor27.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.820
X-RAY DIFFRACTIONp_special_tor85.215
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS

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