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- PDB-1jhk: Crystal structure of the anti-estradiol antibody 57-2 -

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Basic information

Entry
Database: PDB / ID: 1jhk
TitleCrystal structure of the anti-estradiol antibody 57-2
Components
  • Ig gamma-1-chain
  • Ig kappa-chain
KeywordsIMMUNE SYSTEM / antibody / steroid
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / IgG immunoglobulin complex / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / blood microparticle / defense response to bacterium / immune response / external side of plasma membrane / extracellular space / extracellular exosome / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
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
Ig gamma-1 chain C region, membrane-bound form / Anti-colorectal carcinoma light chain / : / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsLamminmaki, U. / Kankare, J.A.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Crystal structure of a recombinant anti-estradiol Fab fragment in complex with 17beta -estradiol.
Authors: Lamminmaki, U. / Kankare, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray analysis of a recombinant Fab fragment in complex with 17-beta-estradiol
Authors: Lamminmaki, U. / Kankare, J.A.
History
DepositionJun 28, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
L: Ig kappa-chain
H: Ig gamma-1-chain


Theoretical massNumber of molelcules
Total (without water)47,1252
Polymers47,1252
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-20 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.267, 64.456, 165.702
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 Ig kappa-chain


Mass: 23665.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCOMB3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: Q8VCP0, UniProt: Q7TS98*PLUS
#2: Antibody Ig gamma-1-chain


Mass: 23460.309 Da / Num. of mol.: 1 / Fragment: residues 1-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCOMB3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL-1 blue / References: UniProt: P01869, UniProt: Q99LC4*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: PEG4000, PEG8000, Tris-HCl, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Details: used microseeding / PH range low: 9.5 / PH range high: 9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115-25 mg/mlprotein1drop
210-14 %PEG40001reservoiror 8-12% PEG8000
3Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200HB / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 17081 / Num. obs: 17081 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.052
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.078 / % possible all: 72.7
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 91.8 %
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Combination of the PDB entries 1TET (variable heavy domain) and 1FDL (variable light domain and both constant domains)

1tet

1fdl


Resolution: 2.51→46.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 650567.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1173 6.9 %RANDOM
Rwork0.198 ---
obs0.23 17081 92.4 %-
all-17081 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.58 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-17.92 Å20 Å20 Å2
2---7.17 Å20 Å2
3----10.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.51→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 0 162 3377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.332 153 7 %
Rwork0.248 2022 -
obs--71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 6.9 % / Rfactor all: 0.23 / Rfactor obs: 0.201 / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Rfactor Rfree: 0.344 / % reflection Rfree: 7 % / Rfactor Rwork: 0.248 / Rfactor obs: 0.258

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