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- PDB-8hbb: Crystal structure of Caenorhabditis elegans NMAD-1 in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hbb | ||||||
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Title | Crystal structure of Caenorhabditis elegans NMAD-1 in complex with ligand III | ||||||
![]() | DNA N6-methyl adenine demethylase | ||||||
![]() | OXIDOREDUCTASE / NMAD-1A / GENE REGULATION | ||||||
Function / homology | ![]() DNA N6-methyladenine demethylase activity / DNA N6-methyladenine demethylase / positive regulation of egg-laying behavior / positive regulation of fertilization / meiotic chromosome condensation / contractile ring / positive regulation of chromosome organization / demethylation / positive regulation of meiosis I / broad specificity oxidative DNA demethylase activity ...DNA N6-methyladenine demethylase activity / DNA N6-methyladenine demethylase / positive regulation of egg-laying behavior / positive regulation of fertilization / meiotic chromosome condensation / contractile ring / positive regulation of chromosome organization / demethylation / positive regulation of meiosis I / broad specificity oxidative DNA demethylase activity / demethylase activity / actomyosin structure organization / positive regulation of double-strand break repair / actin binding / midbody / DNA replication / oxidoreductase activity / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shang, G. / Chen, Z. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A. Authors: Shang, G. / Yang, M. / Li, M. / Ma, L. / Liu, Y. / Ma, J. / Chen, Y. / Wang, X. / Fan, S. / Xie, M. / Wu, W. / Dai, S. / Chen, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185.2 KB | Display | ![]() |
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PDB format | ![]() | 145 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.2 MB | Display | ![]() |
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Full document | ![]() | 3.2 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hazC ![]() 8hb2C 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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Unit cell |
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Components
#1: Protein | Mass: 33220.957 Da / Num. of mol.: 4 / Mutation: E109K, Q112K, Q114K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8MNT9, DNA N6-methyladenine demethylase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 4000, 100 mM Na Caco pH 5.6 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 6, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 35949 / % possible obs: 90.9 % / Redundancy: 5.8 % / CC1/2: 0.959 / Net I/σ(I): 14.84 |
Reflection shell | Resolution: 3.05→3.15 Å / Num. unique obs: 26900 / CC1/2: 0.959 |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 3.09→47.18 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 28.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→47.18 Å
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Refine LS restraints |
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LS refinement shell |
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