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Yorodumi- PDB-3lln: Comparison between the orthorhombic an tetragonal form of the hep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lln | ||||||
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Title | Comparison between the orthorhombic an tetragonal form of the heptamer sequence d(GCG(xT)GCG)/d(CGCACGC). | ||||||
Components |
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Keywords | DNA / DOUBLE HELIX / CENA / SUGAR MODIFICATION / RIGHT-HANDED | ||||||
Function / homology | COBALT HEXAMMINE(III) / DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Robeyns, K. / Herdewijn, P. / Van Meervelt, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2010 Title: Comparison between the orthorhombic and tetragonal forms of the heptamer sequence d[GCG(xT)GCG]/d(CGCACGC) Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L. #1: Journal: J.Am.Chem.Soc. / Year: 2008 Title: Structure of the fully modified left-handed cyclohexene nucleic acid sequence GTGTACAC. Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L. #2: Journal: Nucleic Acids Res. / Year: 2008 Title: Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG). Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L. #3: Journal: Artificial DNA / Year: 2010 Title: Direct observation of two cyclohexenyl (CeNA) ring conformations in duplex DNA Authors: Robeyns, K. / Herdewijn, P. / Van Meervelt, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lln.cif.gz | 18.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lln.ent.gz | 11.6 KB | Display | PDB format |
PDBx/mmJSON format | 3lln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/3lln ftp://data.pdbj.org/pub/pdb/validation_reports/ll/3lln | HTTPS FTP |
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-Related structure data
Related structure data | 3fl6S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 2164.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED ON SOLID SUPPORT |
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#2: DNA chain | Mass: 2083.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHESIZED ON SOLID SUPPORT |
#3: Chemical | ChemComp-NCO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 10%(V/V) 2-METHYL-2,4-PENTANEDIOL(MPD), 20MM COBALT HEXAMINE, 40MM POTASSIUM CACODYLATE BUFFERED AT PH=5.5, AND 80/12MM KCL/NACL, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9537 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 6, 2007 / Details: mirror |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 3→18.55 Å / Num. all: 681 / Num. obs: 681 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 12.4 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 4.5 / Num. unique all: 93 / Rsym value: 0.174 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FL6 (one biological unit) Resolution: 3→18.15 Å / Cor.coef. Fo:Fc: 0.96 / SU B: 14.93 / SU ML: 0.291 / Isotropic thermal model: ISOTROPIC / Cross valid method: NONE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 71.704 Å2
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Refinement step | Cycle: LAST / Resolution: 3→18.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.001→3.079 Å / Total num. of bins used: 20
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