+Open data
-Basic information
Entry | Database: PDB / ID: 1a36 | ||||||
---|---|---|---|---|---|---|---|
Title | TOPOISOMERASE I/DNA COMPLEX | ||||||
Components |
| ||||||
Keywords | ISOMERASE/DNA / COMPLEX (ISOMERASE-DNA) / 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 / chromosome segregation ...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 / chromosome segregation / protein-DNA complex / circadian regulation of gene expression / P-body / fibrillar center / circadian rhythm / chromosome / single-stranded DNA binding / double-stranded DNA binding / peptidyl-serine phosphorylation / perikaryon / DNA replication / chromatin remodeling / response to xenobiotic stimulus / phosphorylation / 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 / RIGID BODY REFINEMENT / Resolution: 2.8 Å | ||||||
Authors | Stewart, L. / Redinbo, M.R. / Qiu, X. / Champoux, J.J. / Hol, W.G.J. | ||||||
Citation | Journal: Science / Year: 1998 Title: A model for the mechanism of human topoisomerase I. Authors: Stewart, L. / Redinbo, M.R. / Qiu, X. / Hol, W.G. / Champoux, J.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a36.cif.gz | 148.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a36.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a36_validation.pdf.gz | 383.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1a36_full_validation.pdf.gz | 407.4 KB | Display | |
Data in XML | 1a36_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1a36_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a36 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a36 | HTTPS FTP |
-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: 70022.859 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN AND C-TERMINAL DOMAIN / Mutation: Y723F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: NUCLEUS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase |
#4: Water | ChemComp-HOH / |
Compound details | NOTE THAT RESIDUES 174 - 214 AND 634 - 640 OF CHAIN A ARE DISORDERED AND ARE NOT PRESENT IN THE ...NOTE THAT RESIDUES 174 - 214 AND 634 - 640 OF CHAIN A ARE DISORDERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.21 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.7 / Details: pH 7.70 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: May 1, 1995 / Details: UNKNOWN |
Radiation | Monochromator: UNKNOWN / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 21217 / % possible obs: 94.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.055 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.305 / % possible all: 86.8 |
Reflection | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 94.7 % / Redundancy: 3 % / Num. measured all: 63314 |
Reflection shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 86.8 % / Redundancy: 2.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: RIGID BODY REFINEMENT Starting model: RECONSTITUTED HUMAN TOPOISOMERASE I COVALENT COMPLEX WITH 22 BASE PAIR DUPLEX DNA Resolution: 2.8→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.84 Å / Total num. of bins used: 25
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 5.5 % |