+Open data
-Basic information
Entry | Database: PDB / ID: 8i6k | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of hMNDA HIN with dsDNA | ||||||
Components |
| ||||||
Keywords | DNA BINDING PROTEIN/DNA / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information negative regulation of B cell proliferation / cellular response to interferon-beta / cellular defense response / activation of innate immune response / B cell receptor signaling pathway / azurophil granule lumen / double-stranded DNA binding / ficolin-1-rich granule lumen / positive regulation of apoptotic process / intracellular membrane-bounded organelle ...negative regulation of B cell proliferation / cellular response to interferon-beta / cellular defense response / activation of innate immune response / B cell receptor signaling pathway / azurophil granule lumen / double-stranded DNA binding / ficolin-1-rich granule lumen / positive regulation of apoptotic process / intracellular membrane-bounded organelle / DNA damage response / Neutrophil degranulation / nucleolus / extracellular exosome / extracellular region / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Li, Y.L. / Jin, T.C. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 Title: Structural mechanism of dsDNA recognition by the hMNDA HIN domain: New insights into the DNA-binding model of a PYHIN protein. Authors: Li, Y. / Zhang, C. / Samad, A. / Zheng, P. / Li, Y. / Chen, F. / Jin, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8i6k.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8i6k.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 8i6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8i6k_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8i6k_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8i6k_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 8i6k_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/8i6k ftp://data.pdbj.org/pub/pdb/validation_reports/i6/8i6k | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24462.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MNDA / Plasmid: pET30a / Details (production host): MBP tag / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41218 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: DNA chain | Mass: 3665.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.93 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1 M Sodium malonate pH 8.0, 0.1 M Tris pH 8.0, 30% w/v Polyethylene glycol 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→13.07 Å / Num. obs: 9936 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03794 / Rpim(I) all: 0.01866 / Rrim(I) all: 0.04245 / Net I/av σ(I): 30.5 / Net I/σ(I): 30.5 |
Reflection shell | Resolution: 2.4→2.486 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3563 / Mean I/σ(I) obs: 2.94 / Num. unique obs: 955 / CC1/2: 0.864 / CC star: 0.963 / Rpim(I) all: 0.2234 / Rrim(I) all: 0.4225 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→13.07 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.7 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→13.07 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell |
|