+Open data
-Basic information
Entry | Database: PDB / ID: 8pmv | ||||||
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Title | transcription factor BARHL2 bound to TAAGC DNA sequence | ||||||
Components |
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Keywords | TRANSCRIPTION / homeobox transcription factor BARHL2 / DNA-binding domain / protein-DNA complex | ||||||
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: 2.1 Å | ||||||
Authors | Morgunova, E. / Popov, A. / Yin, Y. / 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. / Popov, A. / Yin, Y. / Taipale, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pmv.cif.gz | 221.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pmv.ent.gz | 174.1 KB | Display | PDB format |
PDBx/mmJSON format | 8pmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pmv_validation.pdf.gz | 487.6 KB | Display | wwPDB validaton report |
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Full document | 8pmv_full_validation.pdf.gz | 499.3 KB | Display | |
Data in XML | 8pmv_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 8pmv_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pm/8pmv ftp://data.pdbj.org/pub/pdb/validation_reports/pm/8pmv | HTTPS FTP |
-Related structure data
Related structure data | 8pm5C 8pm7C 8pmcC 8pmfC 8pmnC 8pn4C 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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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 7539.536 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BARHL2 / Plasmid: pET20A-SBP / Details (production host): vector / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY43 #2: DNA chain | Mass: 3678.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #3: DNA chain | Mass: 3647.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #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: 2.74 Å3/Da / Density % sol: 57.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: PEG 4000, sodium malonate, 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: 2.1→46.63 Å / Num. obs: 38886 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.054 / Rrim(I) all: 0.132 / Χ2: 0.97 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.1→2.16 Å / % possible obs: 97.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 5.172 / Num. measured all: 18000 / Num. unique obs: 3154 / CC1/2: 0.087 / Rpim(I) all: 2.322 / Rrim(I) all: 5.681 / Χ2: 0.96 / Net I/σ(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.63 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / SU B: 25.69 / SU ML: 0.282 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.199 / 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: 62.801 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→46.63 Å
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