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- PDB-2r56: Crystal Structure of a Recombinant IgE Fab Fragment in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 2r56
TitleCrystal Structure of a Recombinant IgE Fab Fragment in Complex with Bovine Beta-Lactoglobulin Allergen
Components
  • Beta-lactoglobulin
  • IgE Fab Fragment, heavy chain
  • IgE Fab Fragment, light chain
KeywordsIMMUNE SYSTEM / Allergen / IgE / Epitope / Immunocomplex / Lipocalin / Fab / Milk protein / Polymorphism / Retinol-binding / Secreted / Transport
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulins ...Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsNiemi, M. / Kallio, J.M. / Hakulinen, N. / Rouvinen, J.
CitationJournal: Structure / Year: 2007
Title: Molecular interactions between a recombinant IgE antibody and the beta-lactoglobulin allergen.
Authors: Niemi, M. / Jylha, S. / Laukkanen, M.L. / Soderlund, H. / Makinen-Kiljunen, S. / Kallio, J.M. / Hakulinen, N. / Haahtela, T. / Takkinen, K. / Rouvinen, J.
History
DepositionSep 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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: Beta-lactoglobulin
L: IgE Fab Fragment, light chain
H: IgE Fab Fragment, heavy chain
B: Beta-lactoglobulin
M: IgE Fab Fragment, light chain
I: IgE Fab Fragment, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7508
Polymers129,7286
Non-polymers1,0212
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.040, 100.640, 168.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-lactoglobulin / / Beta-LG / Allergen Bos d 5


Mass: 18301.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: LGB / Production host: Escherichia coli (E. coli) / Strain (production host): RV308 / References: UniProt: P02754
#2: Antibody IgE Fab Fragment, light chain


Mass: 23116.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody IgE Fab Fragment, heavy chain


Mass: 23446.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 14 % PEG3350, 0.1 M BTP, n-dodecyl-beta-D-maltoside, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 28740 / Num. obs: 28674 / % possible obs: 99.8 % / Redundancy: 7.2 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.159 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 3.54 / Rsym value: 0.552 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB, 1B8E

1dfb

1b8e


Resolution: 2.8→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1431 5 %random
Rwork0.246 ---
obs-28627 100 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 27.432 Å2
Baniso -1Baniso -2Baniso -3
1--14.633 Å20 Å20 Å2
2--4.029 Å20 Å2
3---10.605 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9066 0 70 0 9136
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.239
X-RAY DIFFRACTIONc_mcbond_it1.3861.5
X-RAY DIFFRACTIONc_scbond_it1.6072
X-RAY DIFFRACTIONc_mcangle_it2.4732
X-RAY DIFFRACTIONc_scangle_it2.5492.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5lmt_xplor.parlmt_xplor.top

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