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- PDB-4x51: X-ray structure of mouse interleukin-10 mutant - S1_E8del, C149Y -

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Basic information

Entry
Database: PDB / ID: 4x51
TitleX-ray structure of mouse interleukin-10 mutant - S1_E8del, C149Y
ComponentsInterleukin-10
KeywordsIMMUNE SYSTEM / cytokine / interleukin-10 family / helix bundle
Function / homology
Function and homology information


Interleukin-10 signaling / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of myeloid dendritic cell activation / positive regulation of B cell apoptotic process / chronic inflammatory response to antigenic stimulus / response to inactivity / negative regulation of membrane protein ectodomain proteolysis / positive regulation of plasma cell differentiation ...Interleukin-10 signaling / negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of myeloid dendritic cell activation / positive regulation of B cell apoptotic process / chronic inflammatory response to antigenic stimulus / response to inactivity / negative regulation of membrane protein ectodomain proteolysis / positive regulation of plasma cell differentiation / response to carbon monoxide / negative regulation of heterotypic cell-cell adhesion / interleukin-10-mediated signaling pathway / negative regulation of cytokine production involved in immune response / negative regulation of MHC class II biosynthetic process / branching involved in labyrinthine layer morphogenesis / negative regulation of nitric oxide biosynthetic process / negative regulation of interleukin-12 production / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of immunoglobulin production / cellular response to hepatocyte growth factor stimulus / negative regulation of B cell proliferation / regulation of synapse organization / defense response to protozoan / positive regulation of sprouting angiogenesis / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of interleukin-6 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of endothelial cell apoptotic process / response to glucocorticoid / positive regulation of cell cycle / positive regulation of endothelial cell proliferation / negative regulation of autophagy / liver regeneration / cytokine activity / positive regulation of cytokine production / response to activity / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / cellular response to estradiol stimulus / positive regulation of miRNA transcription / negative regulation of inflammatory response / regulation of gene expression / cellular response to lipopolysaccharide / protein dimerization activity / defense response to bacterium / response to xenobiotic stimulus / negative regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / extracellular space
Similarity search - Function
Interleukin-10 / Interleukin-10 family / Interleukin 10 / Interleukin-10/19/20/22/24/26 family / Interleukin-10, conserved site / Interleukin-10 family signature. / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKuenze, G.
CitationJournal: To Be Published
Title: X-ray structure of mouse interleukin-10 mutant - S1_E8del, C149Y
Authors: Kuenze, G.
History
DepositionDec 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 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-10
B: Interleukin-10


Theoretical massNumber of molelcules
Total (without water)38,4442
Polymers38,4442
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-75 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.770, 80.820, 84.320
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: Protein Interleukin-10 / IL-10 / Cytokine synthesis inhibitory factor / CSIF


Mass: 19222.205 Da / Num. of mol.: 2 / Fragment: UNP residues 27-178 / Mutation: S1_E8del, C149Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il10, Il-10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P18893
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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

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Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystals grew at 20-30% (v/v) glycerolethoxylate, 0.2M ammonium acetate, 0.1M MES (pH 6.3 - 6.8). Crystals appeared after 1-2 days and reached their final size after 3-4 days.
PH range: 6.3 - 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.05→42.15 Å / Num. obs: 17734 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.3
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LK3

1lk3


Resolution: 2.05→42.15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.236 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24632 902 5.1 %RANDOM
Rwork0.18816 ---
obs0.1911 16785 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---1.57 Å20 Å2
3---1.91 Å2
Refinement stepCycle: LAST / Resolution: 2.05→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 0 57 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192385
X-RAY DIFFRACTIONr_bond_other_d0.0010.022343
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.973192
X-RAY DIFFRACTIONr_angle_other_deg0.86435407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.8724.915118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98115491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1851512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0993.4241136
X-RAY DIFFRACTIONr_mcbond_other3.1013.421135
X-RAY DIFFRACTIONr_mcangle_it4.3025.1031418
X-RAY DIFFRACTIONr_mcangle_other4.3015.1071419
X-RAY DIFFRACTIONr_scbond_it4.2174.0411249
X-RAY DIFFRACTIONr_scbond_other4.2154.0441250
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6555.8351772
X-RAY DIFFRACTIONr_long_range_B_refined8.32927.3412856
X-RAY DIFFRACTIONr_long_range_B_other8.30427.3182849
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 76 -
Rwork0.24 1210 -
obs--99.92 %

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