[English] 日本語
Yorodumi- PDB-4art: STRUCTURE OF THE ORF273 PROTEIN FROM THE ACIDIANUS TWO-TAILED VIRUS -
+Open data
-Basic information
Entry | Database: PDB / ID: 4art | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE ORF273 PROTEIN FROM THE ACIDIANUS TWO-TAILED VIRUS | ||||||
Components | STRUCTURAL PROTEIN ORF273Structure | ||||||
Keywords | VIRAL PROTEIN / ARCHAEAL VIRUS / EXTREMOPHILES / BICAUDAVIRUS / HYPER-THERMOSTABILITY | ||||||
Function / homology | : / Acidianus two-tailed virus, ORF273 protein / virion component / Structural protein ORF273 Function and homology information | ||||||
Biological species | ACIDIANUS TWO-TAILED VIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Felisberto-Rodrigues, C. / Ortiz-Lombardia, M. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal Structure of Atv(Orf273), a New Fold for a Thermo-and Acido-Stable Protein from the Acidianus Two-Tailed Virus. Authors: Felisberto-Rodrigues, C. / Blangy, S. / Goulet, A. / Vestergaard, G. / Cambillau, C. / Garrett, R.A. / Ortiz-Lombardia, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4art.cif.gz | 209.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4art.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 4art.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/4art ftp://data.pdbj.org/pub/pdb/validation_reports/ar/4art | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33023.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACIDIANUS TWO-TAILED VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): T7 EXPRESS IQ PLYSS / References: UniProt: Q3V4T6 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.72 % Description: SOLEIL DATASET (SE-SAD) WAS USED TO SOLVE THE STRUCTURE AND IN THE REFINEMENT OF THE FIRST MODEL. ESRF DATASET USED IMPROVE THE RESOLUTION TO 2.15 A, IN LATER REFINEMENT CYCLES. |
---|---|
Crystal grow | pH: 6 Details: PROTEIN SOLUTION AT 5 MG/ML IN 10 MM BICINE PH 8.5 AND 100 MM NACL WAS MIXED IN A 3:1 RATIO TO A SOLUTION CONTAINING 3.6% ISOPROPANOL AND 1.9 M AMMONIUM SULPHATE AS PRECIPITANT AGENTS IN 5 MM MGCL2 AND 2 MM AMP |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation |
| |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 32549 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24 | |||||||||||||||
Reflection shell | Resolution: 2.15→2.21 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.72 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 2.15→28.42 Å / SU R Cruickshank DPI: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.185 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY RESIDUES 44-54 AND 75- 82 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAPS.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.04 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.354 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→28.42 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.22 Å / Total num. of bins used: 16
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|