+Open data
-Basic information
Entry | Database: PDB / ID: 4jhb | ||||||
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Title | Crystal structure of RelB double mutants: Y300F/I335F | ||||||
Components | Transcription factor RelB | ||||||
Keywords | TRANSCRIPTION / intertwined dimer / non-canonical 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 / lymphocyte differentiation / 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 ...T-helper 1 cell differentiation / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / lymphocyte differentiation / 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 / centrosome / negative regulation of DNA-templated transcription / synapse / chromatin / protein kinase binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Huang, D.B. / Vu, D. / Ghosh, G. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of RelB double mutants: Y300F/I335F Authors: Huang, D.B. / Vu, D. / Ghosh, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jhb.cif.gz | 38.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jhb.ent.gz | 25.7 KB | Display | PDB format |
PDBx/mmJSON format | 4jhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jh/4jhb ftp://data.pdbj.org/pub/pdb/validation_reports/jh/4jhb | HTTPS FTP |
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-Related structure data
Related structure data | 1zk9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12418.055 Da / Num. of mol.: 1 / Fragment: Dimerization domain / Mutation: Y300F, I335F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Relb / References: UniProt: Q04863 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 62.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Jul 2, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.44→50 Å / Num. all: 6185 / Num. obs: 5543 / % possible obs: 88.8 % / Observed criterion σ(F): 1 / Redundancy: 4.4 % / Biso Wilson estimate: 48.1 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.4 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1zk9 Resolution: 2.44→28.45 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 348568.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.3414 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.44→28.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.6 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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