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Open data
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Basic information
Entry | Database: PDB / ID: 1d20 | ||||||
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Title | SOLUTION STRUCTURE OF PHAGE LAMBDA HALF-OPERATOR DNA | ||||||
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![]() | DNA / DOUBLE HELIX / PHAGE LAMBDA HALF-OPERATOR | ||||||
Function / homology | DNA![]() | ||||||
Method | SOLUTION NMR / ENERGY MINIMIZATION, MOLECULAR DYNAMICS | ||||||
![]() | Baleja, J.D. / Sykes, B.D. | ||||||
![]() | ![]() Title: Solution structure of phage lambda half-operator DNA by use of NMR, restrained molecular dynamics, and NOE-based refinement. Authors: Baleja, J.D. / Pon, R.T. / Sykes, B.D. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 22.1 KB | Display | ![]() |
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PDB format | ![]() | 12.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 237.5 KB | Display | ![]() |
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Full document | ![]() | 237.3 KB | Display | |
Data in XML | ![]() | 3.3 KB | Display | |
Data in CIF | ![]() | 4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 2979.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / ![]() |
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#2: DNA chain | Mass: 3109.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / ![]() |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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Sample preparation
Crystal grow | *PLUS Method: other |
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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 0.19 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 0.19 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 |