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Open data
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Basic information
Entry | Database: PDB / ID: 8hcs | ||||||
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Title | zebrafish IRF-11 DBD | ||||||
![]() | Interferon regulatory factor | ||||||
![]() | DNA BINDING PROTEIN / zebrafish / IRF / DBD | ||||||
Function / homology | ![]() anatomical structure development / immune system process / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Z.X. / Zhang, Y.A. / Ouyang, S.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Danio rerio IRF10 and IRF11 bound DNA reveal determinants of interferon regulation Authors: Wang, Z.X. / Liu, B. / Ouyang, S.Y. / Zhang, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.9 KB | Display | ![]() |
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PDB format | ![]() | 20.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.7 KB | Display | ![]() |
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Full document | ![]() | 427 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 6.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hclC ![]() 8hcmC ![]() 2irfS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 13272.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.3 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 1.26 M sodium phosphate monobasic, 0.14 M potassium phosphate dibasic, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 298.15 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 26, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→24.57 Å / Num. obs: 8495 / % possible obs: 90.15 % / Redundancy: 2 % / Biso Wilson estimate: 95.93 Å2 / CC1/2: 1 / Net I/σ(I): 36.4 |
Reflection shell | Resolution: 2.55→2.65 Å / Num. unique obs: 303 / CC1/2: 0.747 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IRF Resolution: 2.75→24.57 Å / SU ML: 0.5488 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.6283 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: 91.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→24.57 Å
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Refine LS restraints |
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LS refinement shell |
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