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- PDB-1jn6: Crystal Structure of Fab-Estradiol Complexes -

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Basic information

Entry
Database: PDB / ID: 1jn6
TitleCrystal Structure of Fab-Estradiol Complexes
Components
  • monoclonal anti-estradiol 10G6D6 Fab heavy chain
  • monoclonal anti-estradiol 10G6D6 Fab light chain
KeywordsIMMUNE SYSTEM / IGG FOLD / ANTIBODY-HAPTEN COMPLEX / ESTRADIOL
Function / homology
Function and homology information


IgG immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / plasma membrane
Similarity search - Function
: / 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
Ig lambda-1 chain C region / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 23, 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 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num
Revision 1.4Aug 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
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: monoclonal anti-estradiol 10G6D6 Fab light chain
B: monoclonal anti-estradiol 10G6D6 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,1382
Polymers46,1382
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.881, 73.119, 142.604
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 monoclonal anti-estradiol 10G6D6 Fab light chain / Fab 10G6 light chain


Mass: 22595.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascetic fluid / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01843*PLUS
#2: Antibody monoclonal anti-estradiol 10G6D6 Fab heavy chain / Fab 10G6 heavy chain


Mass: 23543.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascetic fluid / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6PF95*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPEG 550, Imidazole Malate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-15 mg/mlprotein1drop
222.5 %(w/w)PEG550 MME1reservoir
3200 mMimidazole-malate1reservoirpH7.0
410 mg/mlFab'1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 16156 / Num. obs: 13479 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 67.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.8 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.346 / % possible all: 81.3
Reflection
*PLUS
Num. measured all: 149861 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
% possible obs: 81.3 % / Rmerge(I) obs: 0.346

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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: 1mfc & 1gig

1mfc

1gig


Resolution: 2.7→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.305 660 Random
Rwork0.223 --
all0.246 14619 -
obs0.24 13157 -
Refine analyzeLuzzati sigma a obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 0 29 3213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d1.65

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