+Open data
-Basic information
Entry | Database: PDB / ID: 1aq3 | |||||||||
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Title | BACTERIOPHAGE MS2 CAPSID PROTEIN/RNA COMPLEX | |||||||||
Components |
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Keywords | Virus/RNA / COMPLEX (COAT PROTEIN-RNA) / COAT PROTEIN / RNA-BINDING / VIRAL PROTEIN CAPSID / RNA FRAGMENT / 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 | Enterobacterio phage MS2 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Van Den Worm, S. / Stonehouse, N. / Valegard, K. / Liljas, L. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 1998 Title: Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments. Authors: van den Worm, S.H. / Stonehouse, N.J. / Valegard, K. / Murray, J.B. / Walton, C. / Fridborg, K. / Stockley, P.G. / Liljas, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aq3.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aq3.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 1aq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/1aq3 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/1aq3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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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: 6062.657 Da / Num. of mol.: 2 / Fragment: REPLICASE OPERATOR HAIRPIN, 19 NUCLEOTIDES / Source method: obtained synthetically Keywords: FRAGMENT:REPLICASE OPERATOR HAIRPIN, 19 NUCLEOTIDES References: GenBank: J02467 #2: Protein | Mass: 13724.438 Da / Num. of mol.: 3 / Mutation: T59S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacterio phage MS2 (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal grow | pH: 7.4 / Details: pH 7.40 | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 37 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→25 Å / Num. obs: 159163 / % possible obs: 63 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 2.8 / % possible all: 25 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 25 Å / % possible obs: 63.2 % / Redundancy: 1.8 % |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.87 Å / % possible obs: 25.1 % / Redundancy: 1.1 % / Num. unique obs: 4585 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: REFINED MODEL OF MS2 PROTEIN CAPSID Resolution: 2.8→10 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 17.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.85 Å /
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.204 / Rfactor Rfree: 0.253 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.272 |