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Yorodumi- PDB-8jkn: T95R mutant IRF4 DNA-binding domain bound to an DNA containing GA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jkn | ||||||
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Title | T95R mutant IRF4 DNA-binding domain bound to an DNA containing GAAA motif | ||||||
Components |
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Keywords | TRANSCRIPTION / IRF4 / transcription factor / protein-DNA complex | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | ||||||
Authors | Wang, G. / Feng, X. / Ding, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Structure / Year: 2023 Title: Molecular basis for the functional roles of the multimorphic T95R mutation of IRF4 causing human autosomal dominant combined immunodeficiency. Authors: Wang, G. / Feng, X. / Ding, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jkn.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jkn.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 8jkn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/8jkn ftp://data.pdbj.org/pub/pdb/validation_reports/jk/8jkn | HTTPS FTP |
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-Related structure data
Related structure data | 8jklC 8jkoC 8jkqC 8jksC 7jm4S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 5800.805 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #2: DNA chain | Mass: 5848.765 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: Protein | Mass: 13646.490 Da / Num. of mol.: 4 / Fragment: DNA-binding domain / Mutation: T95R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IRF4, hCG_20902 / Production host: Escherichia coli (E. coli) / References: UniProt: F2Z3D5 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1 M MgCl2, 0.1 M sodium citrate (pH 5.0) and 15% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9752 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 13, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9752 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→102.75 Å / Num. obs: 27994 / % possible obs: 100 % / Redundancy: 15.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.068 / Rrim(I) all: 0.27 / Χ2: 1.01 / Net I/σ(I): 12.2 / Num. measured all: 432182 |
Reflection shell | Resolution: 2.92→3.07 Å / % possible obs: 100 % / Redundancy: 16.1 % / Rmerge(I) obs: 1.769 / Num. measured all: 64448 / Num. unique obs: 4003 / CC1/2: 0.683 / Rpim(I) all: 0.448 / Rrim(I) all: 1.826 / Χ2: 0.95 / Net I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JM4 Resolution: 2.92→48.75 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.92→48.75 Å
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Refine LS restraints |
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LS refinement shell |
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