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- PDB-7utt: Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP... -
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Basic information
Entry | Database: PDB / ID: 7utt | ||||||
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Title | Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination | ||||||
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![]() | Transferase/DNA / non-hydrolyzable ATP (ApCpp) / Transferase-DNA complex | ||||||
Function / homology | ![]() regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway ...regulation of type I interferon production / cyclic GMP-AMP synthase / 2',3'-cyclic GMP-AMP synthase activity / paracrine signaling / poly-ADP-D-ribose modification-dependent protein binding / negative regulation of DNA repair / regulation of immunoglobulin production / cGAS/STING signaling pathway / regulation of T cell activation / negative regulation of cGAS/STING signaling pathway / cGMP-mediated signaling / cellular response to exogenous dsRNA / regulation of immune response / positive regulation of type I interferon production / negative regulation of double-strand break repair via homologous recombination / nucleosome binding / positive regulation of defense response to virus by host / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / cAMP-mediated signaling / molecular condensate scaffold activity / determination of adult lifespan / positive regulation of cellular senescence / site of double-strand break / double-stranded DNA binding / defense response to virus / nuclear body / DNA repair / innate immune response / DNA damage response / chromatin binding / GTP binding / protein homodimerization activity / DNA binding / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() DNA molecule (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, S. / Gabelli, S.B. / Sohn, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Non-hydrolyzable ATP (ApCpp) binds to Cyclic GMP AMP synthase (cGAS) through Mn coordination Authors: Wu, S. / Gabelli, S.B. / Sohn, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 388.2 KB | Display | ![]() |
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PDB format | ![]() | 308.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 31.7 KB | Display | |
Data in CIF | ![]() | 46.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4lezS S: Starting model for refinement |
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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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Unit cell |
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Components
-Protein / DNA chain , 2 types, 6 molecules ACEFIJ
#1: Protein | Mass: 42640.254 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Details (production host): His*6-MBP-Tev-AgeI-mcGAS CAT, Kanamycin resistance Production host: ![]() ![]() #2: DNA chain | Mass: 5514.603 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ordered from IDT / Source: (gene. exp.) DNA molecule (others) / Production host: DNA molecule (others) |
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-Non-polymers , 4 types, 318 molecules ![](data/chem/img/APC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-MN / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.81 % / Description: 0.3mm, polarizes nicely |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium acetate, 32% MPD, with 0.1 M Bis-Tris pH 6.5 PH range: 6.0-7.0 / Temp details: 4-degree Celsius in cold room |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: nitrogen gas stream / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2021 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: horizontal bounce Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→29.67 Å / Num. obs: 69038 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LEZ Resolution: 2.04→29.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.214 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 138.54 Å2 / Biso mean: 46.58 Å2 / Biso min: 19.97 Å2
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Refinement step | Cycle: final / Resolution: 2.04→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.09 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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