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

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Basic information

Entry
Database: PDB / ID: 1jnh
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/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/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
ESTRADIOL-6 CARBOXYL-METHYL-OXIME / Ig lambda-1 chain C region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 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 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_nat ...entity / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
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 ...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

Downloads & links

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Assembly

Deposited unit
A: monoclonal anti-estradiol 10G6D6 Fab light chain
B: monoclonal anti-estradiol 10G6D6 Fab heavy chain
C: monoclonal anti-estradiol 10G6D6 Fab light chain
D: monoclonal anti-estradiol 10G6D6 Fab heavy chain
E: monoclonal anti-estradiol 10G6D6 Fab light chain
F: monoclonal anti-estradiol 10G6D6 Fab heavy chain
G: monoclonal anti-estradiol 10G6D6 Fab light chain
H: monoclonal anti-estradiol 10G6D6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,56012
Polymers185,1228
Non-polymers1,4384
Water97354
1
A: monoclonal anti-estradiol 10G6D6 Fab light chain
B: monoclonal anti-estradiol 10G6D6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6403
Polymers46,2812
Non-polymers3591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-30 kcal/mol
Surface area18450 Å2
MethodPISA
2
C: monoclonal anti-estradiol 10G6D6 Fab light chain
D: monoclonal anti-estradiol 10G6D6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6403
Polymers46,2812
Non-polymers3591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-29 kcal/mol
Surface area18710 Å2
MethodPISA
3
E: monoclonal anti-estradiol 10G6D6 Fab light chain
F: monoclonal anti-estradiol 10G6D6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6403
Polymers46,2812
Non-polymers3591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-29 kcal/mol
Surface area18830 Å2
MethodPISA
4
G: monoclonal anti-estradiol 10G6D6 Fab light chain
H: monoclonal anti-estradiol 10G6D6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6403
Polymers46,2812
Non-polymers3591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-30 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.200, 192.900, 71.120
Angle α, β, γ (deg.)90.00, 92.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
monoclonal anti-estradiol 10G6D6 Fab light chain / Fab 10G6 light chain


Mass: 22737.230 Da / Num. of mol.: 4 / 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.: 4 / Source method: isolated from a natural source / Details: ascetic fluid / Source: (natural) Mus musculus (house mouse)
#3: Chemical
ChemComp-ECO / ESTRADIOL-6 CARBOXYL-METHYL-OXIME


Mass: 359.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H25NO5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.63 %
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 3, 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: 2.85→40 Å / Num. all: 44407 / Num. obs: 41521 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 60.8 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 7.1
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 92.2
Reflection
*PLUS
Num. measured all: 298099
Reflection shell
*PLUS
% possible obs: 92.2 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDN ENTRY: 1mfc & 1gig

1mfc

1gig


Resolution: 2.85→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1867 -random
Rwork0.198 ---
all-43946 --
obs-36604 83.3 %-
Refine analyzeLuzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12724 0 104 54 12882
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.53
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / σ(F): 2 / Rfactor obs: 0.198
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_deg1.53

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