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Yorodumi- PDB-3ulm: X-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ulm | ||||||
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Title | X-ray Diffraction Studies of Ring Crystals obtained for d(CACGCG).d(CGCGTG): Stage (ii) Hexagonal plates with spots | ||||||
Components | 6-mer DNA | ||||||
Keywords | DNA / Z-type DNA double helix | ||||||
Function / homology | DNA Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Mandal, P.K. / Venkadesh, S. / Gautham, N. | ||||||
Citation | Journal: J.Cryst.Growth / Year: 2012 Title: Ring crystals of oligonucleotides: Growth stages and X-ray diffraction studies Authors: Mandal, P.K. / Chandrasekaran, A.R. / Madhanagopal, B.R. / Venkadesh, S. / Gautham, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ulm.cif.gz | 10.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ulm.ent.gz | 6.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ulm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulm ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 1221.840 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chemically synthesized by M/s Microsynth #2: Water | ChemComp-HOH / | Sequence details | THE ACTUAL DNA SEQUENCE FOR THE THIS STUDY IS D(CACGCG).(CGCGTG) | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1mM DNA, 75mM sodium cacodylate trihydrate buffer (pH 7.0), 0.5mM cobalt hexammine chloride, 0.75mM spermine, equilibrated against 50% methyl pentane diol (MPD) , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.54 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2009 Details: The optics consist in a vertical collimating mirror, a double-crystal Si(111) monochromator followed by a toroidal bendable focussing mirror. |
Radiation | Monochromator: a double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 147 / Num. obs: 147 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.0947 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 3.01→3.12 Å / Redundancy: 6.67 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1 / Num. unique all: 12 / Rsym value: 0.352 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Z-type DNA Dinucleotide step built using InsightII Resolution: 3.01→15.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.835 / SU B: 16.392 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R Free: 0.563 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE DNA OLIGONUCLEOTIDE HAS SIX BASE PAIRS (D(CACGCG).D(CGCGTG)) AND FORMS THE Z-TYPE DOUBLE HELICAL STRUCTURE. THE STRUCTURE HAS STATISTICAL DIS-ORDER AND COMPRISES OF A DINUCLEOTIDE STEP ...Details: THE DNA OLIGONUCLEOTIDE HAS SIX BASE PAIRS (D(CACGCG).D(CGCGTG)) AND FORMS THE Z-TYPE DOUBLE HELICAL STRUCTURE. THE STRUCTURE HAS STATISTICAL DIS-ORDER AND COMPRISES OF A DINUCLEOTIDE STEP IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE DINUCLEOTIDE STEP COULD STAND FOR EITHER CPG/CPG OR CPA/TPG. DUE TO DISORDER, THE DINUCLEOTIDE STEP WAS CONSTRUCTED AS TPG/TPG WHERE THE C5 METHYL GROUP OF THYMINE WAS ASSIGNED OCCUPANCY OF 1/6 AND N2 OF GUANINE WAS ASSIGNED OCCUPANCY OF 5/6.
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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: MASK | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.785 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→15.15 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 3.013→3.088 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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