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- PDB-1emt: FAB ANTIBODY FRAGMENT OF AN C60 ANTIFULLERENE ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1emt
TitleFAB ANTIBODY FRAGMENT OF AN C60 ANTIFULLERENE ANTIBODY
Components
  • IGG ANTIBODY (HEAVY CHAIN)
  • IGG ANTIBODY (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / anti-fullerene antibody / nanotubes
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
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-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsBraden, B.C. / Goldbaum, F.A. / Chen, B.-X. / Erlanger, B.F. / Kirschner, A.N. / Wilson, S.R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: X-ray crystal structure of an anti-Buckminsterfullerene antibody fab fragment: biomolecular recognition of C(60).
Authors: Braden, B.C. / Goldbaum, F.A. / Chen, B.X. / Kirschner, A.N. / Wilson, S.R. / Erlanger, B.F.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Antigenicity of Fullerenes: Antibodies Specific for Fullerenes and Their Characteristics
Authors: Chen, B.-X. / Wilson, S.R. / Das, M. / Couglin, D.J. / Erlanger, B.F.
History
DepositionMar 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG ANTIBODY (LIGHT CHAIN)
H: IGG ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,4572
Polymers46,4572
Non-polymers00
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-18 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 65.745, 65.562
Angle α, β, γ (deg.)90.00, 112.45, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer composed of the light (L) and heavy (H) chains

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Components

#1: Antibody IGG ANTIBODY (LIGHT CHAIN)


Mass: 23785.111 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody IGG ANTIBODY (HEAVY CHAIN)


Mass: 22671.557 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: 10% PEG 8000, 0.1 M citrate, Fab at 7 mg/ml concentration, pH 5.0, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlFab1drop
210 mMTris1drop
310 %PEG80001reservoir
40.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.25 Å / Num. all: 21736 / Num. obs: 19413 / % possible obs: 90 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.09
Reflection
*PLUS
% possible obs: 90 %

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.25→60 Å / σ(F): 1
RfactorNum. reflection
Rfree0.24 1739
Rwork0.18 -
all-21736
obs-17986
Refinement stepCycle: LAST / Resolution: 2.25→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 0 282 3515
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 60 Å / σ(F): 1 / Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.106
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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