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- PDB-3pok: Interleukin-1-beta LBT L3 Mutant -

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Basic information

Entry
Database: PDB / ID: 3pok
TitleInterleukin-1-beta LBT L3 Mutant
ComponentsInterleukin-1 beta
KeywordsCYTOKINE / lanthanide tag / beta trefoil / interleukin / signaling / receptor / extracellular membrane
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of neuroinflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of monocyte chemotactic protein-1 production / positive regulation of p38MAPK cascade / negative regulation of synaptic transmission / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of vascular endothelial growth factor production / positive regulation of cell division / positive regulation of glial cell proliferation / regulation of neurogenesis / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / JNK cascade / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / embryo implantation / astrocyte activation / positive regulation of interleukin-2 production / regulation of insulin secretion / positive regulation of mitotic nuclear division / response to interleukin-1 / negative regulation of insulin receptor signaling pathway / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / Interleukin-1 signaling / negative regulation of neurogenesis / positive regulation of interleukin-6 production / integrin binding / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / positive regulation of inflammatory response / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / apoptotic process / positive regulation of gene expression
Similarity search - Function
Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBarthelmes, K. / Reynolds, A.M. / Peisach, E. / Jonker, H.R.A. / DeNunzio, N.J. / Allen, K.N. / Imperiali, B. / Schwalbe, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Engineering encodable lanthanide-binding tags into loop regions of proteins.
Authors: Barthelmes, K. / Reynolds, A.M. / Peisach, E. / Jonker, H.R. / DeNunzio, N.J. / Allen, K.N. / Imperiali, B. / Schwalbe, H.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta


Theoretical massNumber of molelcules
Total (without water)18,9941
Polymers18,9941
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.595, 42.595, 88.002
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Interleukin-1 beta / IL-1 beta / Catabolin


Mass: 18994.484 Da / Num. of mol.: 1 / Fragment: mature form (UNP residues 117-269)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: P01584
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS HAVE REMOVED NATIVE SEQUENCE KDDK AND INSERTED ENGINEERED SEQUENCE GYIDTNNDGWIEGDELY. THIS ...AUTHORS HAVE REMOVED NATIVE SEQUENCE KDDK AND INSERTED ENGINEERED SEQUENCE GYIDTNNDGWIEGDELY. THIS INSERTION REPRESENTS A LANTHANIDE BINDING TAG (LBT) THAT WAS INSERTED AT THE END OF A LOOP.

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100mM sodium acetate trihydrate pH 4.5, 3.0 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2007
RadiationMonochromator: Nickel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→19.2 Å / Num. all: 33832 / Num. obs: 33108 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9 % / Rsym value: 0.039
Reflection shellResolution: 1.7→1.76 Å / Mean I/σ(I) obs: 4.77 / Rsym value: 0.48 / % possible all: 91

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.17 Å / SU ML: 0.22 / σ(F): 0.02 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 3355 10.13 %
Rwork0.175 --
obs0.1787 33108 97.39 %
all-33832 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.724 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 0 106 1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071333
X-RAY DIFFRACTIONf_angle_d1.1451806
X-RAY DIFFRACTIONf_dihedral_angle_d17.708503
X-RAY DIFFRACTIONf_chiral_restr0.079198
X-RAY DIFFRACTIONf_plane_restr0.005238
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7004-1.76110.26643130.24182763X-RAY DIFFRACTION91
1.7611-1.83160.25293240.21322896X-RAY DIFFRACTION94
1.8316-1.91490.25393200.19122915X-RAY DIFFRACTION95
1.9149-2.01570.18083270.17032989X-RAY DIFFRACTION97
2.0157-2.14190.2173400.17013002X-RAY DIFFRACTION98
2.1419-2.3070.21363360.16582985X-RAY DIFFRACTION99
2.307-2.53870.20763360.17883061X-RAY DIFFRACTION100
2.5387-2.90490.22363560.18053024X-RAY DIFFRACTION100
2.9049-3.65580.20373700.16583057X-RAY DIFFRACTION100
3.6558-19.17120.17773330.15313061X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -15.8574 Å / Origin y: -5.2276 Å / Origin z: -9.284 Å
111213212223313233
T0.13 Å20.0033 Å20.0252 Å2-0.1099 Å2-0.0079 Å2--0.1025 Å2
L1.3357 °20.8786 °2-0.3851 °2-3.2902 °2-1.8013 °2--2.5145 °2
S0.0068 Å °-0.125 Å °0.0683 Å °-0.0856 Å °0.0868 Å °0.0132 Å °-0.1926 Å °-0.0169 Å °0.0026 Å °
Refinement TLS groupSelection details: chain A

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