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- PDB-1nbp: Crystal Structure Of Human Interleukin-2 Y31C Covalently Modified... -

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Basic information

Entry
Database: PDB / ID: 1nbp
TitleCrystal Structure Of Human Interleukin-2 Y31C Covalently Modified At C31 With 3-Mercapto-1-(1,3,4,9-tetrahydro-B-carbolin-2-yl)-propan-1-one
ComponentsInterleukin-2
KeywordsCYTOKINE / FOUR-HELIX BUNDLE / SMALL MOLECULE COMPLEX
Function / homology
Function and homology information


kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / negative regulation of lymphocyte proliferation / positive regulation of tissue remodeling / negative regulation of T-helper 17 cell differentiation ...kappa-type opioid receptor binding / response to tacrolimus / regulation of T cell homeostatic proliferation / regulation of CD4-positive, alpha-beta T cell proliferation / interleukin-2 receptor binding / glycosphingolipid binding / positive regulation of plasma cell differentiation / 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) / leukocyte activation involved in immune response / positive regulation of isotype switching to IgG isotypes / interleukin-2-mediated signaling pathway / activated T cell proliferation / cell surface receptor signaling pathway via STAT / Interleukin-2 signaling / kinase activator activity / natural killer cell activation / positive regulation of regulatory T cell differentiation / negative regulation of B cell apoptotic process / positive regulation of immunoglobulin production / positive regulation of dendritic spine development / positive regulation of interleukin-17 production / positive regulation of activated T cell proliferation / T cell differentiation / Interleukin receptor SHC signaling / positive regulation of B cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / cytokine activity / growth factor activity / negative regulation of inflammatory response / positive regulation of type II interferon production / positive regulation of inflammatory response / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / carbohydrate binding / RAF/MAP kinase cascade / positive regulation of cell growth / response to ethanol / phospholipase C-activating G protein-coupled receptor signaling pathway / adaptive immune response / transcription by RNA polymerase II / 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-MHC / Interleukin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHyde, J. / Braisted, A.C. / Randal, M. / Arkin, M.R.
CitationJournal: Biochemistry / Year: 2003
Title: Discovery and characterization of cooperative ligand binding in the adaptive region of interleukin-2
Authors: Hyde, J. / Braisted, A.C. / Randal, M. / Arkin, M.R.
History
DepositionDec 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 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
A: Interleukin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7323
Polymers15,3761
Non-polymers3562
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.160, 85.350, 31.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 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) / Gene: IL2 / Plasmid: pRSET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60568
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MHC / 3-MERCAPTO-1-(1,3,4,9-TETRAHYDRO-B-CARBOLIN-2-YL)-PROPAN-1-ONE


Mass: 260.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.19 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, PEG 8k, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 %PEG80001reservoir
20.2 Mammonium sulfate1reservoir

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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: Aug 17, 2001 / Details: mirrors
RadiationMonochromator: yale miorrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 7096 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 17.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5.5 / Num. unique all: 715 / Rsym value: 0.253 / % possible all: 96.9
Reflection
*PLUS
Lowest resolution: 10 Å
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameVersionClassification
d*TREKdata reduction
AMoREphasing
REFMAC5.1.19refinement
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M4A

1m4a


Resolution: 2.2→10 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 6.077 / SU ML: 0.177 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.338 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27734 342 4.9 %RANDOM
Rwork0.22799 ---
all0.23034 7042 --
obs0.23034 6660 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.507 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--1.1 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 23 49 1057
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221025
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1912.0091382
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9875118
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02720
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1650.2474
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0430.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.2243.5604
X-RAY DIFFRACTIONr_mcangle_it3.4076983
X-RAY DIFFRACTIONr_scbond_it3.0614421
X-RAY DIFFRACTIONr_scangle_it4.3157399
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.273 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.332 38
Rwork0.265 613
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS

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