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- PDB-7m2v: Crystallographic Structure of the Rhombohedral Crystal Form of ST... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7m2v | ||||||
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Title | Crystallographic Structure of the Rhombohedral Crystal Form of STMV Grown from Chloride | ||||||
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![]() | VIRUS/RNA / VIRUS-RNA complex | ||||||
Function / homology | Satellite virus coat domain superfamily / viral capsid / structural molecule activity / PHOSPHATE ION / RNA / RNA (> 10) / Coat protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | McPherson, A. | ||||||
![]() | ![]() Title: Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts. Authors: McPherson, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.8 MB | Display | ![]() |
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Full document | ![]() | 5.9 MB | Display | |
Data in XML | ![]() | 175 KB | Display | |
Data in CIF | ![]() | 267.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bklC ![]() 5bknC ![]() 5bkqC ![]() 7m2tC ![]() 7m3rC ![]() 7m3tC ![]() 7m50C ![]() 7m54C ![]() 7m57C ![]() 4oq8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 20 molecules ABCEJMHHIIJJFXDKKGHGGILOKNN
#1: Protein | Mass: 17533.949 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-RNA chain , 2 types, 20 molecules QQhwwTmienxxyySVkUXTTPYffzz
#2: RNA chain | Mass: 3629.032 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Details: arbitrary RNA uridine nucleotide dodecamer / Source: (natural) ![]() #3: RNA chain | Mass: 3905.512 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Details: arbitrary RNA adenine nucleotide dodecamer / Source: (natural) ![]() |
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-Non-polymers , 4 types, 5589 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-PO4 / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % Description: apex truncated triangular plates very similar in appearance to the monoclinic crystal form of the virus. Face perpendicular is the c axis. |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Crystals grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. Drops were equal amounts of a 5 mg/ml virus stock solution buffered at pH 6.5 ...Details: Crystals grown by sitting drop vapor diffusion in Cryschem plates with 0.6 ml reservoirs and 6 to 8 ul drops. Drops were equal amounts of a 5 mg/ml virus stock solution buffered at pH 6.5 with 0.1 M phosphate, and the reservoir solution. The reservoir solution was 4% w/v NaCl in 0.1 M phosphate at pH 6.0. Crystallization was at 4 degrees C. PH range: 4.5 - 7.0 |
-Data collection
Diffraction | Mean temperature: 173 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→55.3 Å / Num. obs: 345430 / % possible obs: 84 % / Redundancy: 4.5 % / Biso Wilson estimate: 11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rsym value: 0.075 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.85 Å / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 9879 / CC1/2: 0.54 / Rsym value: 0.14 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4OQ8 Resolution: 1.8→50 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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LS refinement shell | Resolution: 1.8→1.83 Å /
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Refinement TLS params. | Method: refined / Origin x: 26.0131022284 Å / Origin y: 33.963285073 Å / Origin z: 8.03239322923 Å
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Refinement TLS group | Selection details: all |