+Open data
-Basic information
Entry | Database: PDB / ID: 6td4 | ||||||
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Title | IRF4 DNA-binding domain surface entropy mutant apo structure | ||||||
Components | Interferon regulatory factor 4Interferon regulatory factors | ||||||
Keywords | DNA BINDING PROTEIN / DNA BINDING DOMAIN / SURFACE ENTROPY MUTANT / APO | ||||||
Function / homology | Function and homology information negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of interleukin-2 production ...negative regulation of toll-like receptor signaling pathway / T-helper 17 cell lineage commitment / regulation of T-helper cell differentiation / myeloid dendritic cell differentiation / positive regulation of interleukin-13 production / immune system process / defense response to protozoan / positive regulation of interleukin-10 production / positive regulation of interleukin-4 production / positive regulation of interleukin-2 production / T cell activation / Interferon gamma signaling / Interferon alpha/beta signaling / nucleosome / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / sequence-specific DNA binding / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Tucker, J.A. / Martin, M.P. / Wang, L.Z. / Jennings, C. / Heath, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Cancer-associated mutations in the IRF4 DNA-binding domain confer no disadvantage in DNA-binding affinity and may increase transcriptional activity Authors: Tatum, N.J. / Scott, R. / Doody, G.M. / Hickson, I. / Jennings, C. / Martin, M.P. / Tooze, R.M. / Tucker, J.A. / Wittner, A. / Wang, L.Z. / Wright, E.K. / Wedge, S.R. / Noble, M.E.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6td4.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6td4.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 6td4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/td/6td4 ftp://data.pdbj.org/pub/pdb/validation_reports/td/6td4 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13938.777 Da / Num. of mol.: 1 / Mutation: E45A E46A K47A C99A Source method: isolated from a genetically manipulated source Details: Additional residues at N- and C-termini from cloning Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, MUM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta (DE3) pLysS / References: UniProt: Q15306 |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25 % PEG 3350, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2016 |
Radiation | Monochromator: single bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→39.28 Å / Num. obs: 17568 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 33.56 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.041 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.71→1.78 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2774 / CC1/2: 0.839 / Rrim(I) all: 1.12 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: personal communication Resolution: 1.71→39.28 Å / SU ML: 0.2108 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.9394 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→39.28 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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