+Open data
-Basic information
Entry | Database: PDB / ID: 1r49 | ||||||
---|---|---|---|---|---|---|---|
Title | Human topoisomerase I (Topo70) double mutant K532R/Y723F | ||||||
Components |
| ||||||
Keywords | Isomerase/DNA / Protein / DNA / topoisomerase I / Isomerase-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / phosphorylation ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / phosphorylation / chromosome segregation / protein-DNA complex / P-body / circadian regulation of gene expression / circadian rhythm / fibrillar center / chromosome / double-stranded DNA binding / peptidyl-serine phosphorylation / single-stranded DNA binding / DNA replication / perikaryon / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / protein serine/threonine kinase activity / chromatin binding / nucleolus / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å | ||||||
Authors | Interthal, H. / Quigley, P.M. / Hol, W.G. / Champoux, J.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The role of lysine 532 in the catalytic mechanism of human topoisomerase I. Authors: Interthal, H. / Quigley, P.M. / Hol, W.G. / Champoux, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1r49.cif.gz | 155.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1r49.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r49_validation.pdf.gz | 445.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1r49_full_validation.pdf.gz | 475.6 KB | Display | |
Data in XML | 1r49_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 1r49_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r49 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r49 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: DNA chain | Mass: 6790.468 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#2: DNA chain | Mass: 6705.373 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 70180.055 Da / Num. of mol.: 1 / Fragment: Topo70 / Mutation: K532R, Y723F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: PEG 3350 MME, Magnesium chloride, MES, TCEP, pH 7.5, VAPOR DIFFUSION, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM |
---|---|
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.13→50 Å / Num. obs: 15514 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.13→3.26 Å / Rsym value: 0.28 / % possible all: 64.7 |
Reflection | *PLUS Highest resolution: 3.1 Å / Num. obs: 15497 / Redundancy: 3.2 % / Rmerge(I) obs: 0.14 |
Reflection shell | *PLUS % possible obs: 64.7 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.13→47.67 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.841 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.656 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.598 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.13→47.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.13→3.211 Å / Total num. of bins used: 20 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Rfactor Rfree: 0.339 / Rfactor Rwork: 0.277 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|