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- PDB-3egb: Structure of Pellino2 FHA domain at 3.3 Angstroms resolution. -

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Basic information

Entry
Database: PDB / ID: 3egb
TitleStructure of Pellino2 FHA domain at 3.3 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 / positive regulation of protein phosphorylation / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical NF-kappaB signal transduction ...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 / positive regulation of protein phosphorylation / protein polyubiquitination / ubiquitin protein ligase activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 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 1.4Aug 30, 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 / 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: Protein pellino homolog 2
B: Protein pellino homolog 2


Theoretical massNumber of molelcules
Total (without water)62,8202
Polymers62,8202
Non-polymers00
Water00
1
A: Protein pellino homolog 2


Theoretical massNumber of molelcules
Total (without water)31,4101
Polymers31,4101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein pellino homolog 2


Theoretical massNumber of molelcules
Total (without water)31,4101
Polymers31,4101
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.676, 89.484, 125.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31410.199 Da / Num. of mol.: 2 / Fragment: UNP residues 7-289,FHA domain
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

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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: 1.95 Å3/Da / Density % sol: 37.01 %
Crystal growTemperature: 295 K / pH: 5.5
Details: 0.05 M sodium citrate, 23% w/v PEG 3350 MME, 1 M NaCl, 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-D / Wavelength: 0.9793
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.25→41 Å / Num. obs: 8337 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 19
Reflection shellResolution: 3.25→3.38 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.5 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.25 Å42.15 Å
Translation3.25 Å42.15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EGA

3ega


Resolution: 3.25→41 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.823 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R Free: 0.671 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.315 380 4.6 %RANDOM
Rwork0.238 ---
obs0.242 7839 99.83 %-
all-7849 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.291 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20 Å2
2--0.89 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 3.25→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 0 0 3244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213305
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9384512
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.895448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5722.522115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.25215428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3661520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022492
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2380.21537
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2711.52264
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.88323558
X-RAY DIFFRACTIONr_scbond_it0.82631041
X-RAY DIFFRACTIONr_scangle_it1.4464.5954
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 40 -
Rwork0.258 551 -
obs--98.5 %

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