+Open data
-Basic information
Entry | Database: PDB / ID: 5cg9 | |||||||||
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Title | NgTET1 in complex with 5mC DNA in space group P3221 | |||||||||
Components |
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Keywords | OXIDOREDUCTASE/DNA / dioxygenase / 5-methylcytosine / NgTET1 / OXIDOREDUCTASE-DNA complex | |||||||||
Function / homology | Function and homology information methylcytosine dioxygenase / 5-methylcytosine dioxygenase activity / double-stranded methylated DNA binding / iron ion binding Similarity search - Function | |||||||||
Biological species | Naegleria gruberi (eukaryote) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.693 Å | |||||||||
Authors | Hashimoto, H. / Pais, J.E. / Dai, N. / Zhang, X. / Zheng, Y. / Cheng, X. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2015 Title: Structure of Naegleria Tet-like dioxygenase (NgTet1) in complexes with a reaction intermediate 5-hydroxymethylcytosine DNA. Authors: Hashimoto, H. / Pais, J.E. / Dai, N. / Correa, I.R. / Zhang, X. / Zheng, Y. / Cheng, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cg9.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cg9.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/5cg9 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/5cg9 | HTTPS FTP |
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-Related structure data
Related structure data | 5cg8C 4lt5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 30725.766 Da / Num. of mol.: 2 / Fragment: UNP residues 57-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_55029 / Plasmid: pET28b-His-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: D2W6T1 |
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-DNA chain , 2 types, 4 molecules BECF
#2: DNA chain | Mass: 3334.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 4021.636 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 5 types, 23 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% (w/v) polyethylene glycol 8000, 200 mM Mg oxaloacetate, 100 mM Na cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HS / Detector: CCD / Date: Jun 14, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→30 Å / Num. all: 29462 / Num. obs: 29462 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.154 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.69→2.79 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 2.2 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LT5 Resolution: 2.693→29.742 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.2 / 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: 2.693→29.742 Å
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Refine LS restraints |
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LS refinement shell |
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