+Open data
-Basic information
Entry | Database: PDB / ID: 1zdj | |||||||||
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Title | STRUCTURE OF BACTERIOPHAGE COAT PROTEIN-LOOP RNA COMPLEX | |||||||||
Components |
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Keywords | Virus/RNA / COAT PROTEIN-RNA COMPLEX / 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: 2.9 Å | |||||||||
Authors | Grahn, E. / Stonehouse, N. / Valegard, K. / Vandenworm, S. / Liljas, L. | |||||||||
Citation | Journal: RNA / Year: 1999 Title: Crystallographic studies of RNA hairpins in complexes with recombinant MS2 capsids: implications for binding requirements. Authors: Grahn, E. / Stonehouse, N.J. / Murray, J.B. / van den Worm, S. / Valegard, K. / Fridborg, K. / 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 | 1zdj.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zdj.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 1zdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zdj_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 1zdj_full_validation.pdf.gz | 463.2 KB | Display | |
Data in XML | 1zdj_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1zdj_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/1zdj ftp://data.pdbj.org/pub/pdb/validation_reports/zd/1zdj | 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: 2525.577 Da / Num. of mol.: 2 / Source method: obtained synthetically #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 7 - 14 IN THE ENTRY. IN PUBLICATIONS, THE NUMBERING IS RELATED TO ...THE RNA MOLECULE IS NUMBERED FROM 7 - 14 IN THE ENTRY. IN PUBLICATIO | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal grow | pH: 7.4 / Details: pH 7.40 | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 37 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Valegard, K., (1986) J. Mol. Biol., 190, 587. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 12, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 168328 / % possible obs: 74.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.114 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.28 / % possible all: 41.2 |
Reflection | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 25 Å / % possible obs: 74.1 % / Redundancy: 2.3 % |
Reflection shell | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 2.97 Å / Redundancy: 1.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→10 Å / σ(F): 2 / Details: PARKINSON ET AL. FOR RNA
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Displacement parameters | Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.95 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: 2.9 Å / Lowest resolution: 10 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.3 |