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- PDB-4ize: Crystal Structure of IL-36gamma -

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Basic information

Entry
Database: PDB / ID: 4ize
TitleCrystal Structure of IL-36gamma
ComponentsInterleukin-36 gamma
KeywordsSIGNALING PROTEIN / beta trefoil / innate immune signaling
Function / homology
Function and homology information


Interleukin-36 pathway / interleukin-1 receptor binding / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / immune response / inflammatory response / innate immune response / extracellular space ...Interleukin-36 pathway / interleukin-1 receptor binding / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / immune response / inflammatory response / innate immune response / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / 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
Interleukin-36 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGuenther, S. / Sundberg, E.J.
CitationJournal: J.Immunol. / Year: 2014
Title: Molecular Determinants of Agonist and Antagonist Signaling through the IL-36 Receptor.
Authors: Gunther, S. / Sundberg, E.J.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Nov 20, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-36 gamma


Theoretical massNumber of molelcules
Total (without water)17,1221
Polymers17,1221
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.315, 89.315, 37.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Interleukin-36 gamma / IL-1-related protein 2 / IL-1RP2 / Interleukin-1 epsilon / IL-1 epsilon / Interleukin-1 family ...IL-1-related protein 2 / IL-1RP2 / Interleukin-1 epsilon / IL-1 epsilon / Interleukin-1 family member 9 / IL-1F9 / Interleukin-1 homolog 1 / IL-1H1


Mass: 17121.537 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1E, IL1F9, IL1H1, IL1RP2, IL36G, UNQ2456/PRO5737 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 5000MME, NaAcetate, pH 4.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2012
Details: Shutterless data collection; Fine phi slicing experiments
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 10812 / Num. obs: 10682 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.223 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 26.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.6665.278071740195.9
2.05-2.110.5197.758942750198
2.11-2.170.4628.988378723199.6
2.17-2.240.4110.969038717197.6
2.24-2.310.30613.69176685199.9
2.31-2.390.28114.589002684199
2.39-2.480.26115.6485846561100
2.48-2.580.18819.58174620199.4
2.58-2.70.15422.2578036191100
2.7-2.830.13923.286625557197
2.83-2.980.09231.437483559199.5
2.98-3.160.07535.787077533199.8
3.16-3.380.06341.5365714971100
3.38-3.650.0548.4958174621100
3.65-40.04552.6350844421100
4-4.470.03659.514513381196.2
4.47-5.170.03462.974297353199.7
5.17-6.330.03559.8636433161100
6.33-8.950.03358.572481235195.5
8.95-400.02865.781538150197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.872 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 521 4.88 %
Rwork0.178 --
obs0.1802 10679 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.03 Å2 / Biso mean: 19.4075 Å2 / Biso min: 4.25 Å2
Refinement stepCycle: LAST / Resolution: 2→34.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 0 110 1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071207
X-RAY DIFFRACTIONf_angle_d1.1771645
X-RAY DIFFRACTIONf_chiral_restr0.076189
X-RAY DIFFRACTIONf_plane_restr0.006213
X-RAY DIFFRACTIONf_dihedral_angle_d12.238449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.20250.26411230.21032449257298
2.2025-2.52110.27171440.19682493263799
2.5211-3.1760.24091170.18732545266299
3.176-34.87770.18491370.15842674281199

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