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Yorodumi- PDB-6l76: Crystal structure of the Ni(II)(Chro)2-d(TTGGGCCGAA/TTCGGCCCAA) c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l76 | ||||||
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Title | Crystal structure of the Ni(II)(Chro)2-d(TTGGGCCGAA/TTCGGCCCAA) complex at 2.94 angstrom resolution | ||||||
Components |
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Keywords | DNA / Duplex DNA / GGGGCC motif / nucleotide flipping-out / Hoogsteen base pair | ||||||
Function / homology | Chem-CPH / NICKEL (II) ION / DNA Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å | ||||||
Authors | Hou, M.H. / Jhan, C.R. / Satange, R.B. / Lin, S.M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction. Authors: Jhan, C.R. / Satange, R. / Wang, S.C. / Zeng, J.Y. / Horng, Y.C. / Jin, P. / Neidle, S. / Hou, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l76.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l76.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 6l76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l76_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 6l76_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 6l76_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 6l76_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l76 ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l76 | HTTPS FTP |
-Related structure data
Related structure data | 6l75C 7bpvC 1vaqS S: Starting model for refinement C: citing same article (ref.) |
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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
-DNA chain , 2 types, 4 molecules ADBC
#1: DNA chain | Mass: 3085.028 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: DNA chain | Mass: 3004.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 8 molecules
#3: Polysaccharide | 2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H- ...2,6-dideoxy-4-O-methyl-alpha-D-galactopyranose-(1-3)-(2R,3R,6R)-6-hydroxy-2-methyltetrahydro-2H-pyran-3-yl acetate Source method: isolated from a genetically manipulated source #4: Polysaccharide | 3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol- ...3-C-methyl-4-O-acetyl-alpha-L-Olivopyranose-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol-(1-3)-(2R,5S,6R)-6-methyltetrahydro-2H-pyran-2,5-diol Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 53 molecules
#5: Chemical | ChemComp-CPH / ( #6: Chemical | ChemComp-NI / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 6.12 Å3/Da / Density % sol: 79.9 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1mM TTGGGCCGAA, 1 mM TTCGGCCCAA, 3 mM Chromomycin A3, 6 mM NiSO4, 2.5 mM Spermine,40 mM Sodium cacodylate (pH=7), 4 % PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.99984 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.94→30 Å / Num. obs: 12146 / % possible obs: 98.6 % / Redundancy: 9.3 % / Biso Wilson estimate: 74.54 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.023 / Rrim(I) all: 0.071 / Χ2: 0.909 / Net I/σ(I): 12.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VAQ Resolution: 2.94→25.511 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 214.51 Å2 / Biso mean: 93.8655 Å2 / Biso min: 61.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.94→25.511 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -26.1521 Å / Origin y: 6.1794 Å / Origin z: -14.636 Å
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Refinement TLS group |
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