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- PDB-3b5k: Crystal structure of murine interleukin-5 -

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Basic information

Entry
Database: PDB / ID: 3b5k
TitleCrystal structure of murine interleukin-5
ComponentsInterleukin-5
KeywordsCYTOKINE / 4-helix bundle / Glycoprotein / Growth factor / Secreted
Function / homology
Function and homology information


positive regulation of eosinophil differentiation / interleukin-5 receptor binding / Interleukin receptor SHC signaling / RAF/MAP kinase cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / interleukin-5-mediated signaling pathway / positive regulation of podosome assembly / positive regulation of immunoglobulin production / : / positive regulation of B cell proliferation ...positive regulation of eosinophil differentiation / interleukin-5 receptor binding / Interleukin receptor SHC signaling / RAF/MAP kinase cascade / Interleukin-3, Interleukin-5 and GM-CSF signaling / interleukin-5-mediated signaling pathway / positive regulation of podosome assembly / positive regulation of immunoglobulin production / : / positive regulation of B cell proliferation / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / immune response / positive regulation of DNA-templated transcription / extracellular space
Similarity search - Function
Interleukin-5 / Interleukin 5 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMueller, T.D. / Patino, E.
CitationJournal: To be Published
Title: Crystal structure of murine interleukin-5
Authors: Patino, E. / Kraich, M. / Kotzsch, A. / Saremba, S. / Paschke, A. / Sebald, W. / Mueller, T.D.
History
DepositionOct 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-5
B: Interleukin-5


Theoretical massNumber of molelcules
Total (without water)26,1362
Polymers26,1362
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-48 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.193, 47.085, 55.053
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 3 / Auth seq-ID: 7 - 109 / Label seq-ID: 5 - 107

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Interleukin-5 / IL-5 / T-cell replacing factor / TRF / Eosinophil differentiation factor / B-cell growth factor II ...IL-5 / T-cell replacing factor / TRF / Eosinophil differentiation factor / B-cell growth factor II / BCGF- II / Cytotoxic T-lymphocyte inducer


Mass: 13067.996 Da / Num. of mol.: 2 / Mutation: M3L, M7T, M31L, M67R, M107L, M113I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il5 / Plasmid: pET31b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04401
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 26% PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 9, 2006 / Details: VariMax Cu High-Res Multilayer
RadiationMonochromator: Multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→54.7 Å / Num. all: 6951 / Num. obs: 6732 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.35 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.52 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 660 / Rsym value: 0.398 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HUL

1hul


Resolution: 2.5→15.09 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.906 / SU B: 20.992 / SU ML: 0.264 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 345 5.2 %RANDOM
Rwork0.21346 ---
all0.21483 6951 --
obs0.21483 6311 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.497 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å2-0.14 Å2
2---0.05 Å20 Å2
3----0.14 Å2
Refine analyzeLuzzati coordinate error free: 0.386 Å
Refinement stepCycle: LAST / Resolution: 2.5→15.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 0 74 1795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221747
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9732354
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7185209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05223.60586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.5515344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7641518
X-RAY DIFFRACTIONr_chiral_restr0.1260.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021280
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2860.3817
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3290.51160
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2960.5100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3380.348
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.290.514
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.27821078
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15431703
X-RAY DIFFRACTIONr_scbond_it1.2482731
X-RAY DIFFRACTIONr_scangle_it1.9613651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
412tight positional0.120.05
422loose positional0.65
412tight thermal0.240.5
422loose thermal2.1510
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 24 -
Rwork0.311 458 -
obs--94.14 %

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