+Open data
-Basic information
Entry | Database: PDB / ID: 1zdh | |||||||||
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Title | MS2 COAT 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) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | |||||||||
Authors | Valegard, K. / Van Den Worm, S. / Liljas, L. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 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: Journal: Nature / Year: 1994 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: Journal: J.Mol.Biol. / Year: 1993 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zdh.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zdh.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zdh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zdh_validation.pdf.gz | 472.9 KB | Display | wwPDB validaton report |
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Full document | 1zdh_full_validation.pdf.gz | 479.5 KB | Display | |
Data in XML | 1zdh_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1zdh_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zdh ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zdh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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: 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.) Enterobacterio phage MS2 (virus) / Genus: Levivirus / Species: Enterobacteria phage MS2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03612 #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 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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Crystal grow | *PLUS Temperature: 37 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
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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 |
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Refinement | Resolution: 2.7→10 Å / σ(F): 2
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Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.9 Å
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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