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- PDB-3ega: Crystal structure of Pellino2 FHA Domain at 1.8 Angstroms resolution -

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Basic information

Entry
Database: PDB / ID: 3ega
TitleCrystal structure of Pellino2 FHA Domain at 1.8 Angstroms resolution
ComponentsProtein pellino homolog 2
KeywordsPROTEIN BINDING / Pellino / FHA Domain / E3 ubiquitin ligase / substrate binding domain / Phosphoprotein
Function / homology
Function and homology information


regulation of Toll signaling pathway / ubiquitin-ubiquitin ligase activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade ...regulation of Toll signaling pathway / ubiquitin-ubiquitin ligase activity / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / RING-type E3 ubiquitin transferase / Interleukin-1 signaling / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of protein phosphorylation / cytosol
Similarity search - Function
Pellino family / : / : / Pellino, FHA domain / Pellino, RING domain
Similarity search - Domain/homology
E3 ubiquitin-protein ligase pellino homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsFerguson, K.M. / Lin, C. / Schmitz, K.R.
CitationJournal: Structure / Year: 2008
Title: Pellino proteins contain a cryptic FHA domain that mediates interaction with phosphorylated IRAK1.
Authors: Lin, C.C. / Huoh, Y.S. / Schmitz, K.R. / Jensen, L.E. / Ferguson, K.M.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Protein pellino homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4152
Polymers29,3191
Non-polymers961
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Protein pellino homolog 2
hetero molecules

A: Protein pellino homolog 2
hetero molecules

A: Protein pellino homolog 2
hetero molecules

A: Protein pellino homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,6618
Polymers117,2764
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area10170 Å2
ΔGint-115 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.650, 86.137, 162.767
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1-

SO4

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Components

#1: Protein Protein pellino homolog 2 / Pellino-2


Mass: 29319.123 Da / Num. of mol.: 1 / Fragment: UNP residues 15-275, FHA domain / Mutation: V61M, L232M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PELI2 / Plasmid: pET28 derivative (HTUA) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HAT8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M sodium acetate, 26.4% w/v PEG 2000 MME, 0.2 M ammonium sulfate, pH 5.5, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795, 0.9796, 0.9495
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 5, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.94951
ReflectionRedundancy: 8.2 % / Av σ(I) over netI: 37.26 / Number: 221150 / Rmerge(I) obs: 0.1 / Χ2: 3.47 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 27082 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885099.110.07411.1078.9
3.083.8810010.0815.9899
2.693.0810010.1063.8899.1
2.442.6910010.1392.5619.2
2.272.4410010.1751.979.1
2.132.2710010.21.5478.9
2.032.1310010.2491.2838.6
1.942.0310010.3211.1318
1.861.9498.610.4131.0116.3
1.81.8686.910.5150.8813.9
ReflectionResolution: 1.8→50 Å / Num. all: 27082 / Num. obs: 27082 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.1 / Χ2: 3.469 / Net I/σ(I): 37.257
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4 / Num. unique all: 2345 / Χ2: 0.881 / % possible all: 86.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→43.07 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.968 / SU B: 2.335 / SU ML: 0.075 / SU R Cruickshank DPI: 0.122 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.122 / ESU R Free: 0.12
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1364 5 %RANDOM
Rwork0.21 ---
all0.212 27047 --
obs0.212 27047 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.52 Å2 / Biso mean: 25.985 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 5 128 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221744
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9512378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60523.3871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70915293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4751513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021298
X-RAY DIFFRACTIONr_nbd_refined0.2120.2738
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.28
X-RAY DIFFRACTIONr_mcbond_it1.0531.51129
X-RAY DIFFRACTIONr_mcangle_it1.7321801
X-RAY DIFFRACTIONr_scbond_it3.143682
X-RAY DIFFRACTIONr_scangle_it3.9234.5569
LS refinement shellResolution: 1.8→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 74 -
Rwork0.295 1492 -
all-1566 -
obs-1566 78.34 %

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