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- PDB-1jgl: Crystal structure of immunoglobulin Fab fragment complexed with 1... -

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Basic information

Entry
Database: PDB / ID: 1jgl
TitleCrystal structure of immunoglobulin Fab fragment complexed with 17-beta-estradiol
Components
  • Ig gamma-1-chain
  • Ig kappa-chain
KeywordsIMMUNE SYSTEM / antibody / four-center hydrogen bond / steroid
Function / homology
Function and homology information


immune response / extracellular space
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 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
ESTRADIOL / : / Anti-colorectal carcinoma light chain / Pterin-mimicking anti-idiotope kappa chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 26, 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 ...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 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
L: Ig kappa-chain
H: Ig gamma-1-chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3983
Polymers47,1252
Non-polymers2721
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-22 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.207, 64.496, 165.285
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: Q920E6, 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: GenBank: 2072131
#3: Chemical ChemComp-EST / ESTRADIOL


Mass: 272.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.86 %
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

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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: 2.15→50 Å / Num. all: 25614 / Num. obs: 25614 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.135 / % possible all: 71.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Combination PDB entries 1TET (heavy chain variable domain)and 1FDL (light chain variable domain and both constant_1 domains)

1tet

1fdl


Resolution: 2.15→46.28 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 450405.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2529 9.9 %RANDOM
Rwork0.199 ---
all-25614 --
obs-25614 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.54 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1-11.6 Å20 Å20 Å2
2---3.62 Å20 Å2
3----7.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.15→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 0 20 340 3585
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.1
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 310 9.6 %
Rwork0.231 2909 -
obs--68.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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