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

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Basic information

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


B cell differentiation / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 24, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_nat ...diffrn_source / entity_src_nat / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_beg_seq_num ..._diffrn_source.pdbx_synchrotron_site / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 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 (BOUND PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)47,6273
Polymers47,6273
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-33 kcal/mol
Surface area19710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.440, 105.440, 295.790
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 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
#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
#3: Protein/peptide PROTEIN (BOUND PEPTIDE)


Mass: 1029.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 4.8 Å3/Da / Density % sol: 71 %
Crystal growpH: 7.5
Details: 1.8 M (NH4)2 SO4, 0.1 M 3-(N- MORPHOLINO)-PROPANESULFONIC AC, pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlFab1drop
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) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.6→91 Å / Num. obs: 29821 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.076
Reflection
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.107

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Processing

Software
NameClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
CCP4refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HFL

2hfl
PDB Unreleased entry


Resolution: 2.65→90 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.325 2039 7 %RANDOM
Rwork0.277 ---
all-26473 --
obs-26473 98 %-
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.65→90 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 0 25 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5892
X-RAY DIFFRACTIONp_mcangle_it2.823
X-RAY DIFFRACTIONp_scbond_it1.6652
X-RAY DIFFRACTIONp_scangle_it2.793
X-RAY DIFFRACTIONp_plane_restr0.050.024
X-RAY DIFFRACTIONp_chiral_restr0.150.62
X-RAY DIFFRACTIONp_singtor_nbd0.1960.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor25.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.520
X-RAY DIFFRACTIONp_special_tor83.415
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS

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