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- PDB-3bqu: Crystal Structure of the 2F5 Fab'-3H6 Fab Complex -

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Basic information

Entry
Database: PDB / ID: 3bqu
TitleCrystal Structure of the 2F5 Fab'-3H6 Fab Complex
Components
  • 2F5 Fab' heavy chain
  • 2F5 Fab' light chain
  • 3H6 Fab heavy chain
  • 3H6 Fab light chain
KeywordsIMMUNE SYSTEM / BETA SHEET
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin complex / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / defense response to bacterium ...positive regulation of B cell activation / phagocytosis, recognition / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin complex / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / defense response to bacterium / external side of plasma membrane / innate immune response / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
If kappa light chain / Ig heavy chain V region MOPC 104E / Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBryson, S. / Julien, J.-P. / Isenman, D.E. / Kunert, R. / Katinger, H. / Pai, E.F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of the complex between the F(ab)' fragment of the cross-neutralizing anti-HIV-1 antibody 2F5 and the F(ab) fragment of its anti-idiotypic antibody 3H6.
Authors: Bryson, S. / Julien, J.P. / Isenman, D.E. / Kunert, R. / Katinger, H. / Pai, E.F.
History
DepositionDec 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2F5 Fab' light chain
B: 2F5 Fab' heavy chain
C: 3H6 Fab light chain
D: 3H6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,9185
Polymers99,8224
Non-polymers961
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.440, 98.330, 154.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 2F5 Fab' light chain


Mass: 23363.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Antibody 2F5 Fab' heavy chain


Mass: 24955.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PYX1*PLUS
#3: Antibody 3H6 Fab light chain


Mass: 25667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NHM3*PLUS
#4: Antibody 3H6 Fab heavy chain


Mass: 25835.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01756*PLUS
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15-18% PEG 8000, 0.20 M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 2004 / Details: Xenocs optics
RadiationMonochromator: Ni / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 21137 / Num. obs: 19786 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.064 / Net I/σ(I): 15.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.398 / % possible all: 94.2

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Processing

Software
NameClassification
MAR345data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2F5B, 1F11, 1ACY

2f5b

1f11

1acy


Resolution: 3→20 Å / Isotropic thermal model: overall temperature factors / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 948 RANDOM
Rwork0.276 --
all0.276 21137 -
obs0.276 19786 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6317 0 5 0 6322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.00193
X-RAY DIFFRACTIONc_bond_d0.003562

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