+Open data
-Basic information
Entry | Database: PDB / ID: 2c4y | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | MS2-RNA HAIRPIN (2THIOURACIL-5) COMPLEX | |||||||||
Components |
| |||||||||
Keywords | VIRUS/RNA / CAPSID / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL PROTEIN/RNA / VIRUS COAT PROTEIN / RNA- BINDING / ICOSAHEDRAL VIRUS / VIRUS-RNA complex | |||||||||
Function / homology | Function and homology information 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 | Escherichia phage MS2 (virus) ENTEROBACTERIO PHAGE MS2 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | |||||||||
Authors | Grahn, E. / Moss, T. / Helgstrand, C. / Fridborg, K. / Sundaram, M. / Tars, K. / Lago, H. / Stonehouse, N.J. / Davis, D.R. / Stockley, P.G. / Liljas, L. | |||||||||
Citation | Journal: Rna / Year: 2001 Title: Structural basis of pyrimidine specificity in the MS2 RNA hairpin-coat-protein complex. Authors: Grahn, E. / Moss, T. / Helgstrand, C. / Fridborg, K. / Sundaram, M. / Tars, K. / Lago, H. / Stonehouse, N.J. / Davis, D.R. / Stockley, P.G. / Liljas, L. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2c4y.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2c4y.ent.gz | 81.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c4y_validation.pdf.gz | 465.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2c4y_full_validation.pdf.gz | 471 KB | Display | |
Data in XML | 2c4y_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 2c4y_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c4y ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c4y | HTTPS FTP |
-Related structure data
Related structure data | 2bu1C 2c4qC 2c4zC 2c50C 2c51C 2ms2S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar 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: (Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 13738.464 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage MS2 (virus) / Gene: MS2g2 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: C0M1L4, UniProt: P03612*PLUS #2: RNA chain | Mass: 6078.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ENTEROBACTERIO PHAGE MS2 (virus) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 278 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 16, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→30 Å / Num. obs: 212866 / % possible obs: 74 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.16 |
Reflection shell | Resolution: 2.68→2.78 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.21 / % possible all: 10 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MS2 Resolution: 2.68→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.8236 Å2 / ksol: 0.254902 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.68→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.68→2.73 Å / Total num. of bins used: 20
|