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- PDB-6vhi: Crystal structure of the human ILRUN Fw domain -

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Basic information

Entry
Database: PDB / ID: 6vhi
TitleCrystal structure of the human ILRUN Fw domain
ComponentsProtein ILRUN
KeywordsIMMUNE SYSTEM / Fw domain / innate immune system / immunoglobulin fold
Function / homology
Function and homology information


negative regulation of defense response to virus / phagophore assembly site / negative regulation of protein localization to nucleus / negative regulation of type I interferon production / negative regulation of DNA binding / negative regulation of tumor necrosis factor production / ubiquitin binding / macroautophagy / innate immune response / nucleus / cytoplasm
Similarity search - Function
C6orf106, UBA-like domain / Next to BRCA1, central domain / Ig-like domain from next to BRCA1 gene / UBA-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsCaputo, A.T. / Adams, T.E.
CitationJournal: Heliyon / Year: 2020
Title: Molecular characterisation of ILRUN, a novel inhibitor of proinflammatory and antimicrobial cytokines.
Authors: Ambrose, R.L. / Brice, A.M. / Caputo, A.T. / Alexander, M.R. / Tribolet, L. / Liu, Y.C. / Adams, T.E. / Bean, A.G.D. / Stewart, C.R.
History
DepositionJan 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ILRUN


Theoretical massNumber of molelcules
Total (without water)13,3841
Polymers13,3841
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.931, 40.977, 23.291
Angle α, β, γ (deg.)90, 91.43, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein ILRUN / Inflammation and lipid regulator with UBA-like and NBR1-like domains protein


Mass: 13384.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILRUN, C6orf106 / Plasmid: pET43 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H6K1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1 M ammonium sulfate and 0.15 M trisodium citrate-citric acid, pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.45865 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45865 Å / Relative weight: 1
ReflectionResolution: 2.46→67.94 Å / Num. obs: 4775 / % possible obs: 99.9 % / Redundancy: 4.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.061 / Rrim(I) all: 0.134 / Χ2: 0.79 / Net I/σ(I): 7.9
Reflection shellResolution: 2.46→2.59 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 709 / CC1/2: 0.89 / Rpim(I) all: 0.306 / Rrim(I) all: 0.658 / Χ2: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OLE

4ole


Resolution: 2.46→67.94 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.889 / Cross valid method: FREE R-VALUE / SU R Blow DPI: 0.352 / SU Rfree Blow DPI: 0.223 / Details: used LSSR restraints generated from PDB entry 4OLE
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 233 4.88 %RANDOM
Rwork0.1919 ---
obs0.1935 4775 99.9 %-
Displacement parametersBiso mean: 57.77 Å2
Baniso -1Baniso -2Baniso -3
1--24.3081 Å20 Å2-11.9823 Å2
2--15.6118 Å20 Å2
3---8.6964 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.46→67.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms834 0 0 6 840
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011657HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.112988HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d486SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes254HARMONIC5
X-RAY DIFFRACTIONt_it854HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion109SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1174SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion16.32
LS refinement shellResolution: 2.46→2.54 Å
RfactorNum. reflection% reflection
Rfree0.242 21 -
Rwork0.2057 --
obs0.2073 435 100 %
Refinement TLS params.Origin x: 23.6769 Å / Origin y: 14.4436 Å / Origin z: 5.7397 Å
111213212223313233
T0.2483 Å20.0086 Å2-0.0348 Å2--0.1838 Å2-0.0017 Å2---0.2501 Å2
L4.3979 °20.9865 °20.5197 °2-2.1781 °20.1335 °2--3.8925 °2
S0.0186 Å °-0.0675 Å °0.0054 Å °-0.0675 Å °-0.043 Å °-0.3831 Å °0.0054 Å °-0.3831 Å °0.0244 Å °
Refinement TLS groupSelection details: { A|* }

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