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Yorodumi- PDB-9dzm: Dimeric human OCT2 (POU2F2) POU domain bound to palindromic MORE DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 9dzm | ||||||||||||
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Title | Dimeric human OCT2 (POU2F2) POU domain bound to palindromic MORE DNA | ||||||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / transcription factor / protein-DNA complex / TRANSCRIPTION-DNA complex / TRANSCRIPTION | ||||||||||||
Function / homology | Function and homology information humoral immune response / RNA polymerase II transcribes snRNA genes / cellular response to virus / positive regulation of interleukin-6 production / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...humoral immune response / RNA polymerase II transcribes snRNA genes / cellular response to virus / positive regulation of interleukin-6 production / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||||||||
Authors | Terrell, J.R. / Poon, G.M.K. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Coupled heterogeneity to dimeric site-specific binding by the POU-Family Transcription Factor OCT2 Authors: Terrell, J.R. / Poon, G.M.K. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9dzm.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9dzm.ent.gz | 119.6 KB | Display | PDB format |
PDBx/mmJSON format | 9dzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9dzm_validation.pdf.gz | 467.1 KB | Display | wwPDB validaton report |
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Full document | 9dzm_full_validation.pdf.gz | 471.3 KB | Display | |
Data in XML | 9dzm_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 9dzm_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dz/9dzm ftp://data.pdbj.org/pub/pdb/validation_reports/dz/9dzm | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6438.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||||
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#2: DNA chain | Mass: 6751.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||||||
#3: Protein | Mass: 19278.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: POU2F2, OCT2, OTF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P09086 #4: Chemical | ChemComp-BR / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 150 mM KBr, 27.5% PEG MME 2000 mixed 1:1 with 200 uM DNA:protein complex |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2023 |
Radiation | Monochromator: vertical DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.920105 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→33.91 Å / Num. obs: 16395 / % possible obs: 95.45 % / Redundancy: 2.1 % / Biso Wilson estimate: 51.55 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06205 / Rpim(I) all: 0.0564 / Rrim(I) all: 0.08414 / Net I/σ(I): 8.37 |
Reflection shell | Resolution: 2.54→2.631 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4024 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 1603 / CC1/2: 0.87 / CC star: 0.965 / Rpim(I) all: 0.3637 / Rrim(I) all: 0.544 / % possible all: 95.19 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→33.91 Å / SU ML: 0.3803 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 29.7684 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: 66.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.54→33.91 Å
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Refine LS restraints |
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LS refinement shell |
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