+
Open data
-
Basic information
Entry | Database: PDB / ID: 1zdh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MS2 COAT PROTEIN/RNA COMPLEX | |||||||||
![]() |
| |||||||||
![]() | Virus/RNA / COMPLEX (COAT PROTEIN-RNA) / 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 | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Valegard, K. / Van Den Worm, S. / Liljas, L. | |||||||||
![]() | ![]() Title: The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. Authors: Valegard, K. / Murray, J.B. / Stonehouse, N.J. / van den Worm, S. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 79.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 479.5 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| x 60|||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||
3 | ![]()
| x 5|||||||||||||||||||||||||||||||||
4 | ![]()
| x 6|||||||||||||||||||||||||||||||||
5 | ![]()
| |||||||||||||||||||||||||||||||||
6 | ![]()
| x 10|||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
#1: RNA chain | Mass: 6061.673 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #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 1 - 19 IN THE ENTRY. IN PUBLICATIONS, THE NUMBERING IS RELATED TO ...THE RNA MOLECULE IS NUMBERED FROM 1 - 19 IN THE ENTRY. IN PUBLICATIO | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
---|---|
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 210601 / % possible obs: 82 % / Rmerge(I) obs: 0.067 |
Reflection | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8.1 Å / % possible obs: 81.6 % |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 18.8 % / Rmerge(I) obs: 0.215 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.7→10 Å / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|