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- PDB-1hi6: ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1hi6
TitleANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE
Components
  • IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)
  • IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)
  • PEPTIDE 5
KeywordsIMMUNE SYSTEM/PEPTIDE / COMPLEX (ANTIBODY-PEPTIDE) / POLYSPECIFICITY / CROSSREACTIVITY / FAB-FRAGMENT / HIV-1 / IMMUNE SYSTEM-PEPTIDE complex
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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHahn, M. / Wessner, H. / Schneider-Mergener, J. / Hohne, 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
DepositionJan 2, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)
B: IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)
C: PEPTIDE 5


Theoretical massNumber of molelcules
Total (without water)47,8263
Polymers47,8263
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.960, 102.960, 294.090
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 IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)


Mass: 23928.721 Da / Num. of mol.: 1 / 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 IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)


Mass: 22669.508 Da / Num. of mol.: 1 / 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 PEPTIDE 5


Mass: 1227.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: EPITOPE-RELATED PEPTIDE / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNH2: THE SYNTHETIC PEPTIDE HAS ITS C-TERMINAL END BLOCKED WITH AN AMIDE GROUP.
Has protein modificationY
Sequence detailsTHE SEQUENCE IS RELATED TO THE ENTRY 1BOG. THE TWO RESIDUES IN THIS ENTRY VALB168, THRB171 ARE ...THE SEQUENCE IS RELATED TO THE ENTRY 1BOG. THE TWO RESIDUES IN THIS ENTRY VALB168, THRB171 ARE LEU168 AND SER171 RESPECTIVELY IN THE ENTRY 1BOG

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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: 4.7 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP SET UP AT ROOM TEMPERATURE. PROTEIN CONCENTRATION: 10 MG/ML RESERVOIR: 1.8 M AMMONIUM SULFATE, 0.1 M MOPS-BUFFER, PH 7.5.
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.55→90 Å / Num. obs: 2976 / % possible obs: 95.4 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 24.8
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOG

1bog


Resolution: 2.55→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.329 1472 5 %RANDOM
Rwork0.284 ---
obs0.284 29486 95.1 %-
Displacement parametersBiso mean: 44.66 Å2
Baniso -1Baniso -2Baniso -3
1--7.57 Å2-3.79 Å20 Å2
2---7.57 Å20 Å2
3---15.15 Å2
Refinement stepCycle: LAST / Resolution: 2.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 0 59 3419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.522
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.55→2.58 Å / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.371 -5 %
Rwork0.358 1000 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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