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Yorodumi- PDB-2fih: Crystal Structure Analysis of the B-DNA Dodecamer CGCGAA-aU-TCGCG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fih | ||||||||||||||||||
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Title | Crystal Structure Analysis of the B-DNA Dodecamer CGCGAA-aU-TCGCG, with Incorporated Arabino-Uridine (aU) | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Arabinonucleic Acid / Sugar Modifications / B-form DNA | Function / homology | DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å | Authors | Egli, M. / Li, F. | Citation | Journal: Biochemistry / Year: 2006 | Title: 2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H. Authors: Li, F. / Sarkhel, S. / Wilds, C.J. / Wawrzak, Z. / Prakash, T.P. / Manoharan, M. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fih.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fih.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/2fih ftp://data.pdbj.org/pub/pdb/validation_reports/fi/2fih | HTTPS FTP |
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-Related structure data
Related structure data | 2fiiC 2fijC 2filC 355dS 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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Unit cell |
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Details | The biological assembly is a duplex and corresponds to the crystallographic asymmetric unit, hence no symmetry operators are needed |
-Components
#1: DNA chain | Mass: 3665.365 Da / Num. of mol.: 2 / Mutation: Incorporated arabino-U at position 7 / Source method: obtained synthetically #2: Chemical | ChemComp-MG / | #3: 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: 2.16 Å3/Da / Density % sol: 43.12 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / pH: 7 Details: Final droplet composition: 0.6mM oligonucleotide, 20mM sodium cacodylate, 6.3mM Mg(OAc)2, and 3mM spermine tetrahydrochloride., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00 | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.826 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→50 Å / Num. obs: 23845 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.033 |
Reflection shell | Resolution: 1.13→1.17 Å / Rmerge(I) obs: 0.2 / % possible all: 59.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NDB entry BDL084/PDB entry 355D Resolution: 1.13→50 Å / Num. restraintsaints: 15328 / σ(F): 0 Details: The hkl data was processed from 50.0 A(low) to 1.09 A(high) according to the scalepack output. Authors performed the refinement from 50.0 A to 1.13 A, because the last shell (1.13-1.09A) has ...Details: The hkl data was processed from 50.0 A(low) to 1.09 A(high) according to the scalepack output. Authors performed the refinement from 50.0 A to 1.13 A, because the last shell (1.13-1.09A) has a low completeness and was exluded. The low resolution range 50.0A-23.7A might not contain any data.
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Refinement step | Cycle: LAST / Resolution: 1.13→50 Å
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