+Open data
-Basic information
Entry | Database: PDB / ID: 8pn4 | ||||||
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Title | transcription factor BARHL2 bound to DNA sequences | ||||||
Components |
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Keywords | TRANSCRIPTION / transcription factor / DNA-binding / protein-DNA complex / DNA-binding domain | ||||||
Function / homology | Function and homology information amacrine cell differentiation / cell fate determination / regulation of axon extension / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin ...amacrine cell differentiation / cell fate determination / regulation of axon extension / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Morgunova, E. / Yin, Y. / Popov, A. / Taipale, J. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: transcription factor BARHL2 bound to DNA sequences Authors: Morgunova, E. / Yin, Y. / Popov, A. / Taipale, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pn4.cif.gz | 241.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pn4.ent.gz | 190.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pn4_validation.pdf.gz | 496.1 KB | Display | wwPDB validaton report |
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Full document | 8pn4_full_validation.pdf.gz | 502.9 KB | Display | |
Data in XML | 8pn4_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 8pn4_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/8pn4 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/8pn4 | HTTPS FTP |
-Related structure data
Related structure data | 8pm5C 8pm7C 8pmcC 8pmfC 8pmnC 8pmvC 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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Unit cell |
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-Components
#1: Protein | Mass: 7509.488 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pET20A-SBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43 #2: DNA chain | Mass: 3638.379 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 3687.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.66 Å3/Da / Density % sol: 53.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: PEG 4000, sodium acetate, |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.52 Å / Num. obs: 20553 / % possible obs: 99.5 % / Redundancy: 3.8 % / CC1/2: 0.985 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.135 / Rrim(I) all: 0.263 / Χ2: 0.96 / Net I/σ(I): 5.9 / Num. measured all: 78862 |
Reflection shell | Resolution: 2.6→2.72 Å / % possible obs: 97.5 % / Redundancy: 4 % / Rmerge(I) obs: 1.827 / Num. measured all: 9556 / Num. unique obs: 2416 / CC1/2: 0.285 / Rpim(I) all: 1.055 / Rrim(I) all: 2.114 / Χ2: 0.96 / Net I/σ(I) obs: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→39.4 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.933 / SU B: 37.331 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R: 1.234 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.067 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→39.4 Å
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