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- PDB-4jgm: Crystal structure of RelB double mutants: Y300F/I335V -

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Basic information

Entry
Database: PDB / ID: 4jgm
TitleCrystal structure of RelB double mutants: Y300F/I335V
ComponentsTranscription factor RelB
KeywordsTRANSCRIPTION / intertwined dimer / side-by side dimer / transcription factor
Function / homology
Function and homology information


T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interferon-beta production / cellular response to osmotic stress / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / antigen processing and presentation ...T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / CD209 (DC-SIGN) signaling / myeloid dendritic cell differentiation / negative regulation of interferon-beta production / cellular response to osmotic stress / T-helper 1 type immune response / non-canonical NF-kappaB signal transduction / antigen processing and presentation / canonical NF-kappaB signal transduction / transcription repressor complex / response to cytokine / circadian regulation of gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / innate immune response / negative regulation of DNA-templated transcription / centrosome / synapse / chromatin / protein kinase binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain ...Transcription factor RelB / RelB leucine zipper / RelB transactivation domain / RelB leucine zipper / RelB transactivation domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transcription factor RelB
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHuang, D.B. / Vu, D. / Ghosh, G.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: A structural basis for selective dimerization by NF-kappa B RelB.
Authors: Vu, D. / Huang, D.B. / Vemu, A. / Ghosh, G.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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Assembly

Deposited unit
A: Transcription factor RelB


Theoretical massNumber of molelcules
Total (without water)12,3701
Polymers12,3701
Non-polymers00
Water97354
1
A: Transcription factor RelB

A: Transcription factor RelB


Theoretical massNumber of molelcules
Total (without water)24,7402
Polymers24,7402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.940, 65.940, 65.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Transcription factor RelB


Mass: 12370.012 Da / Num. of mol.: 1 / Fragment: Dimerization domain / Mutation: Y300F, I335V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: Q04863
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jul 2, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 3488 / Num. obs: 3061 / % possible obs: 88 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.088
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3-3.173.40.512.6495199.5
3.17-3.383.40.286.55031100
3.38-3.663.50.199.35271100
3.66-4.073.40.0912.1509199
4.07-4.763.40.0715527199
4.76-6.463.30.0619.5532198
6.46-503.30.0622385198

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Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1zk9

1zk9


Resolution: 3→29.43 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 104419.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 158 5.2 %RANDOM
Rwork0.211 ---
obs0.211 3061 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 82.3674 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 91.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.43 Å20 Å20 Å2
2--10.43 Å20 Å2
3----20.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms867 0 0 54 921
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.852
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.061 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 19 5.1 %
Rwork0.255 356 -
obs--67.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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