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Open data
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Basic information
Entry | Database: PDB / ID: 1zdj | |||||||||
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Title | STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX | |||||||||
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![]() | Virus/RNA / COAT PROTEIN-RNA COMPLEX / COAT PROTEIN / RNA-BINDING / VIRAL PROTEIN CAPSID / RNA FRAGMENT / Icosahedral virus / Virus-RNA COMPLEX | |||||||||
Function / homology | ![]() negative regulation of viral translation / T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Grahn, E. / Stonehouse, N. / Valegard, K. / Vandenworm, S. / Liljas, L. | |||||||||
![]() | ![]() Title: Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements. Authors: Grahn, E. / Stonehouse, N.J. / Murray, J.B. / van den Worm, S. / Valegard, K. / Fridborg, K. / Stockley, P.G. / Liljas, L. #1: ![]() Title: Crystal Structure of an RNA Bacteriophage Coat Protein-Operator Complex Authors: Valegard, K. / Murray, J.B. / Stockley, P.G. / Stonehouse, N.J. / Liljas, L. #2: ![]() Title: The Refined Structure of Bacteriophage MS2 at 2.8 A Resolution Authors: Golmohammadi, R. / Valegard, K. / Fridborg, K. / Liljas, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94 KB | Display | ![]() |
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PDB format | ![]() | 74.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458 KB | Display | ![]() |
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Full document | ![]() | 463.2 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 |
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: RNA chain | Mass: 2525.577 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 13738.464 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | Sequence details | THE RNA MOLECULE IS NUMBERED FROM 7 - 14 IN THE ENTRY. IN PUBLICATIONS, THE NUMBERING IS RELATED TO ...THE RNA MOLECULE IS NUMBERED FROM 7 - 14 IN THE ENTRY. IN PUBLICATIO | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | pH: 7.4 / Details: pH 7.40 | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 37 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Valegard, K., (1986) J. Mol. Biol., 190, 587. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 168328 / % possible obs: 74.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.114 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / % possible all: 41.2 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 25 Å / % possible obs: 74.1 % / Redundancy: 2.3 % |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 2.97 Å / Redundancy: 1.6 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.95 Å
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |