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- PDB-4p0k: Crystal Structure of Double Loop-Swapped Interleukin-36Ra -

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Basic information

Entry
Database: PDB / ID: 4p0k
TitleCrystal Structure of Double Loop-Swapped Interleukin-36Ra
ComponentsInterleukin-36 receptor antagonist/Interleukin-36 gamma chimera protein
KeywordsCYTOKINE / chimeric protein / Interleukin
Function / homology
Function and homology information


interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity ...interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Interleukin-1 receptor antagonist/Interleukin-36 / 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
Interleukin-36 gamma / Interleukin-36 receptor antagonist protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsGuenther, S. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
American Asthma Foundation13-0066 United States
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
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Oct 4, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords / symmetry
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.4Sep 27, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-36 receptor antagonist/Interleukin-36 gamma chimera protein


Theoretical massNumber of molelcules
Total (without water)16,9151
Polymers16,9151
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.115, 43.115, 119.122
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Interleukin-36 receptor antagonist/Interleukin-36 gamma chimera protein


Mass: 16915.205 Da / Num. of mol.: 1 / Mutation: V2S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBH0, UniProt: Q9NZH8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 1.89 Å3/Da / Density % sol: 34.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 25% (w/v) PEG5000MME, 0.1 M NaAcetate, pH 5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.7→37.34 Å / Num. obs: 14865 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 18.49 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.034 / Net I/σ(I): 14.8 / Num. measured all: 117020
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 2.2 / Num. measured all: 5540 / Num. unique all: 782 / Rpim(I) all: 0.331 / Rejects: 0 / % possible all: 99.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
XDSdata scaling
Aimlessdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1md6

1md6


Resolution: 1.7→37.339 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 735 4.96 %Random selection
Rwork0.195 14083 --
obs0.1968 14818 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.48 Å2 / Biso mean: 25.8822 Å2 / Biso min: 8.44 Å2
Refinement stepCycle: final / Resolution: 1.7→37.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 123 1247
Biso mean---30.76 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071149
X-RAY DIFFRACTIONf_angle_d1.0761554
X-RAY DIFFRACTIONf_chiral_restr0.047168
X-RAY DIFFRACTIONf_plane_restr0.005202
X-RAY DIFFRACTIONf_dihedral_angle_d15.568423
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.83070.30111470.248927492896
1.8307-2.01490.22771450.206627672912
2.0149-2.30650.23291460.187427842930
2.3065-2.90570.22881440.209728132957
2.9057-37.34770.22371530.179529703123

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