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Yorodumi- PDB-1d18: SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d18 | ||||||||||||||||||
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Title | SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED REFINEMENT | ||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / DOUBLE HELIX | Function / homology | DNA | Function and homology information Method | SOLUTION NMR / ENERGY MINIMIZATION, MOLECULAR DYNAMICS | Authors | Baleja, J.D. / Sykes, B.D. | Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Solution conformation of purine-pyrimidine DNA octamers using nuclear magnetic resonance, restrained molecular dynamics and NOE-based refinement. Authors: Baleja, J.D. / Germann, M.W. / van de Sande, J.H. / Sykes, B.D. #1: Journal: J.Magn.Reson. / Year: 1990 Title: Distance Measurement and Structure Refinement with Noe Data Authors: Baleja, J.D. / Moult, J. / Sykes, B.D. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d18.cif.gz | 19 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d18.ent.gz | 10.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d18_validation.pdf.gz | 237.5 KB | Display | wwPDB validaton report |
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Full document | 1d18_full_validation.pdf.gz | 237.3 KB | Display | |
Data in XML | 1d18_validation.xml.gz | 3 KB | Display | |
Data in CIF | 1d18_validation.cif.gz | 3.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/1d18 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/1d18 | 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 chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
NMR software | Name: GROMOS / Developer: DE VLIEG ET AL / Classification: refinement |
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Refinement | Method: ENERGY MINIMIZATION, MOLECULAR DYNAMICS / Software ordinal: 1 Details: THE STRUCTURE WAS REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.23 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES ...Details: THE STRUCTURE WAS REFINED AGAINST PRIMARY NOE DATA. THE R VALUE IS 0.23 OVER ALL OBSERVED, QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR FOR NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR CALCULATIONS. FURTHER DETAILS ARE GIVEN IN REFERENCE 1. |
NMR ensemble | Conformers submitted total number: 1 |