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- PDB-1hh9: ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1hh9
TitleANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE
Components
  • IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)
  • IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)
  • PEP-2
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: 2.7 Å
AuthorsHahn, M. / Wessner, H. / Schneider-Mergener, J. / Hohne, W.
Citation
Journal: Embo J. / Year: 2000
Title: Evolutionary Transition Pathways for Changing Peptide Ligand Specificity and Structure
Authors: Hoffmuller, U. / Knaute, T. / Hahn, M. / Hohne, W. / Schneider-Mergener, J. / Kramer, A.
#1: Journal: 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
DepositionDec 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 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 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 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 1.7Nov 6, 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: PEP-2


Theoretical massNumber of molelcules
Total (without water)47,7843
Polymers47,7843
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.720, 102.720, 295.240
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 PEP-2


Mass: 1185.285 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.: 52 / 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, VALB171 ARE ...THE SEQUENCE IS RELATED TO THE ENTRY 1BOG. THE TWO RESIDUES IN THIS ENTRY VALB168, VALB171 ARE LEU168 AND LEU171 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: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
30.1 MMOPS1reservoirpH7.5

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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: 2.7→16 Å / Num. obs: 24567 / % possible obs: 95.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 14
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.7 / % possible all: 98.4

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Processing

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

1bog


Resolution: 2.7→16 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.333 1225 5 %RANDOM
Rwork0.282 ---
obs0.282 24567 95.6 %-
Refinement stepCycle: LAST / Resolution: 2.7→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 0 52 3401
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_deg1.5
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PROTEIN.LIMK

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