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Yorodumi- PDB-1dhh: NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dhh | ||||||
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Title | NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC) | ||||||
Components |
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Keywords | DNA-RNA HYBRID / DNA/RNA HYBRID IN DNA DUPLEX | ||||||
Function / homology | DNA / DNA/RNA hybrid Function and homology information | ||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | ||||||
Authors | Nishizaki, T. / Iwai, S. / Ohkubo, T. / Kojima, C. / Nakamura, H. / Kyogoku, Y. / Ohtsuka, E. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). Authors: Nishizaki, T. / Iwai, S. / Ohkubo, T. / Kojima, C. / Nakamura, H. / Kyogoku, Y. / Ohtsuka, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dhh.cif.gz | 17.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dhh.ent.gz | 9.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dhh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dhh_validation.pdf.gz | 238.5 KB | Display | wwPDB validaton report |
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Full document | 1dhh_full_validation.pdf.gz | 238.2 KB | Display | |
Data in XML | 1dhh_validation.xml.gz | 2.1 KB | Display | |
Data in CIF | 1dhh_validation.cif.gz | 2.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/1dhh ftp://data.pdbj.org/pub/pdb/validation_reports/dh/1dhh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA/RNA hybrid | Mass: 2854.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: A SUBSTRATE OF RNASE H / Keywords: RIBONUCLEIC ACID |
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#2: DNA chain | Mass: 2666.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: A SUBSTRATE OF RNASE H / Keywords: DEOXYRIBONUCLEIC ACID/RIBONUCLEIC ACID |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Sample |
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Sample conditions | pH: 7 / Temperature: 298 K | ||||||||||||
Crystal grow | *PLUS Method: other |
-Processing
Software |
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NMR software | Name: X-PLOR / Version: 3.1F / Developer: BRUNGER / Classification: refinement | ||||||||
Refinement | Method: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1 Details: RMSD BOND DISTANCES 0.0077 ANGSTROMS RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 ...Details: RMSD BOND DISTANCES 0.0077 ANGSTROMS RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE STRUCTURES WAS REFINED BY A COMBINATION OF RESTRAINED MOLECULAR DYNAMICS USING THE X-PLOR (V3.1F) PROGRAM (BRUNGER 1988) AND FULL RELAXATION MATRIX REFINEMENT OF THE TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRUM AT 150 MSEC. | ||||||||
NMR ensemble | Conformers submitted total number: 1 |