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

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Basic information

Entry
Database: PDB / ID: 1jnn
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
ESTRADIOL / : / : / Anti-colorectal carcinoma light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 ...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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6443
Polymers46,3722
Non-polymers2721
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-23 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.950, 143.24, 53.37
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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: 22944.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 12658313, UniProt: Q99LC4*PLUS
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.91 %
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 18, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 9432 / Num. obs: 8800 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Biso Wilson estimate: 55.7 Å2 / Rsym value: 0.106 / Net I/σ(I): 8.3
Reflection shellResolution: 3.2→3.3 Å / Mean I/σ(I) obs: 1.8 / Rsym value: 0.478 / % possible all: 90

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 1bbd

1bbd


Resolution: 3.2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.316 490 Random
Rwork0.211 --
all0.235 9432 -
obs0.226 8800 -
Refine analyzeLuzzati sigma a obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 20 0 3263
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d1.65
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.65

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