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- PDB-1m4a: Crystal Structure of Human Interleukin-2 Y31C Covalently Modified... -

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Basic information

Entry
Database: PDB / ID: 1m4a
TitleCrystal Structure of Human Interleukin-2 Y31C Covalently Modified at C31 with (1H-Indol-3-yl)-(2-mercapto-ethoxyimino)-acetic acid
Componentsinterleukin-2Interleukin 2
KeywordsCYTOKINE / four-helix bundle / small molecule complex
Function / homology
Function and homology information


kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / regulation of CD4-positive, alpha-beta T cell proliferation / regulation of T cell homeostatic proliferation / interleukin-2 receptor binding / positive regulation of plasma cell differentiation / response to tacrolimus / glycosphingolipid binding / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of isotype switching to IgG isotypes / leukocyte activation involved in immune response / interleukin-2-mediated signaling pathway / natural killer cell activation / activated T cell proliferation / positive regulation of regulatory T cell differentiation / protein kinase C-activating G protein-coupled receptor signaling pathway / kinase activator activity / negative regulation of B cell apoptotic process / Interleukin-2 signaling / positive regulation of dendritic spine development / positive regulation of activated T cell proliferation / positive regulation of interleukin-17 production / positive regulation of immunoglobulin production / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein phosphorylation / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of type II interferon production / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / RAF/MAP kinase cascade / positive regulation of cell growth / carbohydrate binding / response to ethanol / transcription by RNA polymerase II / adaptive immune response / cell adhesion / immune response / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-2 / Interleukin-2, conserved site / Interleukin 2 / Interleukin-2 signature. / Interleukin-2 family / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MPE / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsArkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. ...Arkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. / Wells, J.A. / Braisted, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Binding of small molecules to an adaptive protein-protein interface
Authors: Arkin, M.A. / Randal, M. / DeLano, W.L. / Hyde, J. / Luong, T.N. / Oslob, J.D. / Raphael, D.R. / Taylor, L. / Wang, J. / McDowell, R.S. / Wells, J.A. / Braisted, A.C.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7343
Polymers15,3761
Non-polymers3582
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.150, 47.590, 42.630
Angle α, β, γ (deg.)90.00, 104.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein interleukin-2 / Interleukin 2 / IL-2 / T-CELL GROWTH FACTOR / TCGF / ALDESLEUKIN


Mass: 15375.948 Da / Num. of mol.: 1 / Mutation: Y31C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60568
#2: Chemical ChemComp-MPE / (1H-INDOL-3-YL)-(2-MERCAPTO-ETHOXYIMINO)-ACETIC ACID


Mass: 266.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N2O3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 1.99 Å3/Da / Density % sol: 38.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 2, 2000 / Details: mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→10 Å / Num. all: 5840 / Num. obs: 5840 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 16.1
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 2 % / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 3.2 / Num. unique all: 438 / Rsym value: 0.246 / % possible all: 67.6

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Processing

Software
NameVersionClassification
d*TREKdata reduction
AMoREphasing
REFMAC5.1.19refinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→10 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.54 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32364 561 9.7 %RANDOM
Rwork0.27124 ---
all0.27625 5210 --
obs0.27625 5210 91.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.652 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å20 Å20.28 Å2
2---0.76 Å20 Å2
3---4.37 Å2
Refinement stepCycle: LAST / Resolution: 2.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 24 13 972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022972
X-RAY DIFFRACTIONr_angle_refined_deg1.3662.0151306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6285111
X-RAY DIFFRACTIONr_chiral_restr0.0950.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02675
X-RAY DIFFRACTIONr_nbd_refined0.2660.2499
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.235
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3460.22
X-RAY DIFFRACTIONr_mcbond_it2.3582.5570
X-RAY DIFFRACTIONr_mcangle_it45930
X-RAY DIFFRACTIONr_scbond_it2.1172.5402
X-RAY DIFFRACTIONr_scangle_it3.4295376
LS refinement shellResolution: 2.181→2.254 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.388 41 -
Rwork0.318 349 -
obs-390 67.6 %

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