+Open data
-Basic information
Entry | Database: PDB / ID: 2bq5 | ||||||
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Title | MS2 (N87AE89K mutant) - RNA hairpin complex | ||||||
Components |
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Keywords | VIRUS/RNA / CAPSID / COMPLEX (CAPSID PROTEIN-RNA HAIRPIN) / HAIRPIN / LEVIVIRUS / VIRUS/VIRAL PROTEIN/RNA / VIRUS COAT PROTEIN / 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 | BACTERIOPHAGE MS2 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. ...Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structural Basis of RNA Binding Discrimination between Bacteriophages Qbeta and MS2. Authors: Horn, W.T. / Tars, K. / Grahn, E. / Helgstrand, C. / Baron, A.J. / Lago, H. / Adams, C.J. / Peabody, D.S. / Phillips, S.E.V. / Stonehouse, N.J. / Liljas, L. / Stockley, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bq5.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bq5.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/2bq5 ftp://data.pdbj.org/pub/pdb/validation_reports/bq/2bq5 | HTTPS FTP |
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-Related structure data
Related structure data | 1zseC 2b2dC 2b2eC 2b2gC 2bnyC 2bs0C 2bs1C 2ms2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13695.505 Da / Num. of mol.: 3 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTERIOPHAGE MS2 (virus) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03612 #2: RNA chain | Mass: 6062.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE MS2 (virus) Compound details | ENGINEERED RESIDUE IN CHAIN A, ASN 87 TO ALA ENGINEERED RESIDUE IN CHAIN A, GLU 89 TO LYS ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 1, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 221184 / % possible obs: 33 % / Observed criterion σ(I): 0 / Redundancy: 1.5 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2MS2 Resolution: 2.91→29.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 9718030.26 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.2797 Å2 / ksol: 0.307294 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.95 Å / Rfactor Rfree error: 0.112 / Total num. of bins used: 20
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Xplor file |
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