+Open data
-Basic information
Entry | Database: PDB / ID: 1a34 | ||||||
---|---|---|---|---|---|---|---|
Title | SATELLITE TOBACCO MOSAIC VIRUS/RNA COMPLEX | ||||||
Components |
| ||||||
Keywords | Virus/RNA / WATER STRUCTURE / RNA / VIRUS ASSEMBLY / MACROMOLECULAR INTERACTIONS / SATELLITE TOBACCO MOSAIC VIRUS / Icosahedral virus / Virus-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Satellite Tobacco Mosaic Virus | ||||||
Method | X-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Larson, S.B. / Day, J. / Greenwood, A.J. / McPherson, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Refined structure of satellite tobacco mosaic virus at 1.8 A resolution. Authors: Larson, S.B. / Day, J. / Greenwood, A. / McPherson, A. #1: Journal: Nature / Year: 1993 Title: Double-Helical RNA in Satellite Tobacco Mosaic Virus Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Three-Dimensional Structure of Satellite Tobacco Mosaic Virus at 2.9 A Resolution Authors: Larson, S.B. / Koszelak, S. / Day, J. / Greenwood, A. / Dodds, J.A. / McPherson, A. #3: Journal: Protein Sci. / Year: 1992 Title: Macromolecular Crystal Growth Experiments on International Microgravity Laboratory--1 Authors: Day, J. / McPherson, A. #4: Journal: J.Mol.Biol. / Year: 1989 Title: Preliminary Analysis of Crystals of Satellite Tobacco Mosaic Virus Authors: Koszelak, S. / Dodds, J.A. / McPherson, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a34.cif.gz | 93.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a34.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a34 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a34 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 60||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 |
| x 5||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 |
| x 6||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
6 |
| x 15||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17533.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Satellite Tobacco Mosaic Virus / Production host: Nicotiana tabacum (common tobacco) / References: UniProt: P17574 |
---|
-RNA chain , 2 types, 2 molecules BC
#2: RNA chain | Mass: 3247.100 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#3: RNA chain | Mass: 3016.700 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 3 types, 170 molecules
#4: Chemical | ChemComp-SO4 / |
---|---|
#5: Chemical | ChemComp-U / |
#6: Water | ChemComp-HOH / |
-Details
Compound details | RNA CHAIN B HAS BEEN DESCRIBED BY AN ARBITRARY 10 NUCLEOTIDE CHAIN COMPOSED OF ADENINE BASES. ...RNA CHAIN B HAS BEEN DESCRIBED BY AN ARBITRARY 10 NUCLEOTIDE |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 20 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 25 % Description: 8 SPACE-GROWN CRYSTALS AND 12 EARTH-GROWN CRYSTALS | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: liquid diffusion in microgravity / pH: 6.5 Details: PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT ...Details: PROTEIN WAS FOUR TIMES RECRYSTALLIZED FROM BULK SOLUTION BY ADDITION AF AMMONIUM SULFATE TO 15% SATURATION. SPACE CRYSTALS WERE GROWN BY LIQUID-LIQUID DIFFUSION IN A MICROGRAVITY ENVIRONMENT OVER 12 DAYS ABOARD IML-I MISSION OF THE US SPACE SHUTTLE., pH 6.50, liquid diffusion in microgravity | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: Koszelak, S., (1989) J.Mol.Biol., 209, 323. / PH range low: 7.5 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 290 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Feb 1, 1992 / Details: NONE |
Radiation | Monochromator: SUPPER GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.81→30 Å / Num. obs: 271689 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 8.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 |
Reflection shell | Resolution: 1.81→1.94 Å / Redundancy: 2.1 % / Rsym value: 0.199 / % possible all: 63.9 |
Reflection | *PLUS Lowest resolution: 9999 Å / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Num. measured all: 2239616 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR, MOLECULAR REPLACEMENT Starting model: MODIFIED STNV Resolution: 1.81→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 4 Details: THE RMS DEVIATIONS LISTED ABOVE ARE FOR THE PROTEIN. RMS DEVIATIONS FOR THE DOUBLE HELICAL RNA ARE THE FOLLOWING: BONDS: 0.021 ANGLES: 3.06 DIHEDRAL ANGLES: 11.12 IMPROPER ANGLES: 2.05 MEAN ...Details: THE RMS DEVIATIONS LISTED ABOVE ARE FOR THE PROTEIN. RMS DEVIATIONS FOR THE DOUBLE HELICAL RNA ARE THE FOLLOWING: BONDS: 0.021 ANGLES: 3.06 DIHEDRAL ANGLES: 11.12 IMPROPER ANGLES: 2.05 MEAN B FOR RNA IS 99.1 AND FOR ALL NON- HYDROGEN ATOMS THE MEAN B IS 37.6. NCS RESTRAINTS WERE APPLIED TO THE RNA BACKBONE ONLY. THREE GROUPS WERE DEFINED: GROUP 1, NUCLEOTIDES 1002 - 1006 AND 1102 - 1106; GROUP 2, 1001, 1007 AND 1101, 1107; GROUP 3, 1000, 1008, 1009 AND 1100, 1108, 1109.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.81→1.9 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.81 Å / Lowest resolution: 30 Å / σ(F): 4 / % reflection Rfree: 1.5 % / Rfactor obs: 0.179 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 1.4 % |