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- PDB-2ilk: CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-10 AT 1.6 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2ilk
TitleCRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-10 AT 1.6 ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-10
KeywordsCYTOKINE
Function / homology
Function and homology information


negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / positive regulation of B cell apoptotic process / : ...negative regulation of chronic inflammatory response to antigenic stimulus / interleukin-10 receptor binding / regulation of response to wounding / negative regulation of cytokine activity / negative regulation of interleukin-18 production / negative regulation of myeloid dendritic cell activation / negative regulation of interferon-alpha production / negative regulation of chemokine (C-C motif) ligand 5 production / 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 / regulation of isotype switching / negative regulation of heterotypic cell-cell adhesion / interleukin-10-mediated signaling pathway / negative regulation of cytokine production involved in immune response / negative regulation of interleukin-1 production / 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-8 production / negative regulation of interleukin-12 production / endothelial cell apoptotic process / 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 heterotypic cell-cell adhesion / leukocyte chemotaxis / type 2 immune response / CD163 mediating an anti-inflammatory response / negative regulation of cytokine production / 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 / Interleukin-10 signaling / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / negative regulation of interleukin-6 production / negative regulation of type II interferon production / B cell proliferation / negative regulation of mitotic cell cycle / negative regulation of tumor necrosis factor production / response to glucocorticoid / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / negative regulation of T cell proliferation / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / negative regulation of autophagy / B cell differentiation / FCGR3A-mediated IL10 synthesis / positive regulation of DNA-binding transcription factor activity / liver regeneration / cytokine activity / positive regulation of cytokine production / response to activity / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / growth factor activity / cellular response to estradiol stimulus / response to molecule of bacterial origin / positive regulation of miRNA transcription / negative regulation of inflammatory response / Signaling by ALK fusions and activated point mutants / regulation of gene expression / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / protein dimerization activity / defense response to bacterium / immune response / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsZdanov, A. / Schalk-Hihi, C. / Wlodawer, A.
Citation
Journal: Protein Sci. / Year: 1996
Title: Crystal structure of human interleukin-10 at 1.6 A resolution and a model of a complex with its soluble receptor.
Authors: Zdanov, A. / Schalk-Hihi, C. / Wlodawer, A.
#1: Journal: Structure / Year: 1995
Title: Crystal Structure of Interleukin-10 Reveals the Functional Dimer with an Unexpected Topological Similarity to Interferon Gamma
Authors: Zdanov, A. / Schalk-Hihi, C. / Gustchina, A. / Tsang, M. / Weatherbee, J. / Wlodawer, A.
History
DepositionJul 1, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: INTERLEUKIN-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9614
Polymers18,6721
Non-polymers2883
Water5,459303
1
A: INTERLEUKIN-10
hetero molecules

A: INTERLEUKIN-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9218
Polymers37,3452
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9940 Å2
ΔGint-158 kcal/mol
Surface area16260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.530, 69.530, 70.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein INTERLEUKIN-10


Mass: 18672.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P22301
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
210 %ammonium sulfate1drop
350 mMsodium cacodylate1drop
460 %satammonium sulfate1reservoir
50.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9575
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 4, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9575 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 27529 / % possible obs: 86.4 % / Observed criterion σ(I): 1 / Redundancy: 10.1 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 1
Reflection
*PLUS
Rmerge(I) obs: 0.072

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
PROFFTrefinement
RefinementResolution: 1.6→10 Å / Num. reflection obs: 21495 / σ(F): 3
Displacement parametersBiso mean: 23.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 15 303 1582
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.017
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.055
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1692.5
X-RAY DIFFRACTIONp_mcangle_it3.0453.5
X-RAY DIFFRACTIONp_scbond_it5.2984
X-RAY DIFFRACTIONp_scangle_it7.8127
X-RAY DIFFRACTIONp_plane_restr0.0160.022
X-RAY DIFFRACTIONp_chiral_restr0.1980.18
X-RAY DIFFRACTIONp_singtor_nbd0.1940.5
X-RAY DIFFRACTIONp_multtor_nbd0.2630.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3320.5
X-RAY DIFFRACTIONp_planar_tor2.83.5
X-RAY DIFFRACTIONp_staggered_tor16.314
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.212
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS

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