+Open data
-Basic information
Entry | Database: PDB / ID: 1a41 | ||||||
---|---|---|---|---|---|---|---|
Title | TYPE 1-TOPOISOMERASE CATALYTIC FRAGMENT FROM VACCINIA VIRUS | ||||||
Components | TOPOISOMERASE I | ||||||
Keywords | ISOMERASE / TYPE 1B TOPOISOMERASE | ||||||
Function / homology | Function and homology information DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / virion component / DNA binding Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å | ||||||
Authors | Cheng, C. / Kussie, P. / Pavletich, N. / Shuman, S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Authors: Cheng, C. / Kussie, P. / Pavletich, N. / Shuman, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a41.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a41.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 1a41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a41_validation.pdf.gz | 378.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1a41_full_validation.pdf.gz | 388.1 KB | Display | |
Data in XML | 1a41_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 1a41_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/1a41 ftp://data.pdbj.org/pub/pdb/validation_reports/a4/1a41 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27274.953 Da / Num. of mol.: 1 / Fragment: CARBOXY-TERMINAL CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus / Genus: Orthopoxvirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68698, DNA topoisomerase |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 5.6 / Details: pH 5.6 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Detector | Type: ADSC / Detector: CCD / Date: Jul 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 13123 / % possible obs: 96.1 % / Observed criterion σ(I): 3 / Rsym value: 0.049 |
Reflection shell | Resolution: 2.3→2.38 Å / Rsym value: 0.224 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 114536 / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS % possible obs: 99.1 % / Rmerge(I) obs: 0.224 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.3→20 Å / σ(F): 3
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |