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- PDB-1jnl: Crystal Structure of Fab-Estradiol Complexes -

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Basic information

Entry
Database: PDB / ID: 1jnl
TitleCrystal Structure of Fab-Estradiol Complexes
Components
  • monoclonal anti-estradiol 17E12E5 immunoglobulin gamma-1 chain
  • monoclonal anti-estradiol 17E12E5 immunoglobulin kappa chain
KeywordsIMMUNE SYSTEM / IGG FOLD / ANTIBODY-HAPTEN COMPLEX / ESTRADIOL
Function / homology
Function and homology information


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
: / : / Anti-colorectal carcinoma light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMonnet, C. / Bettsworth, F. / Stura, E.A. / Le Du, M.-H. / Menez, R. / Derrien, L. / Zinn-Justin, S. / Gilquin, B. / Sibai, G. / Battail-Poirot, N. ...Monnet, C. / Bettsworth, F. / Stura, E.A. / Le Du, M.-H. / Menez, R. / Derrien, L. / Zinn-Justin, S. / Gilquin, B. / Sibai, G. / Battail-Poirot, N. / Jolivet, M. / Menez, A. / Arnaud, M. / Ducancel, F. / Charbonnier, J.B.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Highly specific anti-estradiol antibodies: structural characterisation and binding diversity.
Authors: Monnet, C. / Bettsworth, F. / Stura, E.A. / Du, M.H. / Menez, R. / Derrien, L. / Zinn-Justin, S. / Gilquin, B. / Sibai, G. / Battail-Poirot, N. / Jolivet, M. / Menez, A. / Arnaud, M. / ...Authors: Monnet, C. / Bettsworth, F. / Stura, E.A. / Du, M.H. / Menez, R. / Derrien, L. / Zinn-Justin, S. / Gilquin, B. / Sibai, G. / Battail-Poirot, N. / Jolivet, M. / Menez, A. / Arnaud, M. / Ducancel, F. / Charbonnier, J.B.
History
DepositionJul 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: monoclonal anti-estradiol 17E12E5 immunoglobulin kappa chain
H: monoclonal anti-estradiol 17E12E5 immunoglobulin gamma-1 chain


Theoretical massNumber of molelcules
Total (without water)46,5902
Polymers46,5902
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-20 kcal/mol
Surface area19570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.950, 143.240, 53.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody monoclonal anti-estradiol 17E12E5 immunoglobulin kappa chain / Fab' 17E12 / light chain


Mass: 23426.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 12658311, UniProt: Q7TS98*PLUS
#2: Antibody monoclonal anti-estradiol 17E12E5 immunoglobulin gamma-1 chain / Fab' 17E12 / heavy chain


Mass: 23162.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 12658313, UniProt: Q99LC4*PLUS

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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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.3
Details: PEG 8000, CHES, pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-15 mg/mlprotein1drop
218 %(w/v)PEG80001reservoir
3100 mMCHES1reservoirpH9.3
410 mg/mlF(ab')1reservoir

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 10882 / Num. obs: 10863 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.087 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.1 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.291 / % possible all: 96.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1bbd

1bbd


Resolution: 3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 568 random
Rwork0.195 --
all0.236 11221 -
obs0.206 10862 -
Refine analyzeLuzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 0 3309
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_d1.79
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.79

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