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Yorodumi- PDB-1a31: HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a31 | ||||||
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Title | HUMAN RECONSTITUTED DNA TOPOISOMERASE I IN COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX | ||||||
Components |
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Keywords | ISOMERASE/DNA / TOPOISOMERASE I/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 / response to xenobiotic stimulus => GO:0009410 / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus ...DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / response to xenobiotic stimulus => GO:0009410 / embryonic cleavage / programmed cell death / supercoiled DNA binding / DNA binding, bending / DNA topological change / SUMOylation of DNA replication proteins / male germ cell nucleus / viral process / 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 / MIR WITH ANOMALOUS SCATTERING / Resolution: 2.1 Å | ||||||
Authors | Redinbo, M.R. / Stewart, L. / Kuhn, P. / Champoux, J.J. / Hol, W.G.J. | ||||||
Citation | Journal: Science / Year: 1998 Title: Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Authors: Redinbo, M.R. / Stewart, L. / Kuhn, P. / Champoux, J.J. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a31.cif.gz | 138.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a31.ent.gz | 108.9 KB | Display | PDB format |
PDBx/mmJSON format | 1a31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a31_validation.pdf.gz | 391.6 KB | Display | wwPDB validaton report |
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Full document | 1a31_full_validation.pdf.gz | 409.5 KB | Display | |
Data in XML | 1a31_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1a31_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a31 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a31 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 7452.674 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 7161.867 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 70118.844 Da / Num. of mol.: 1 / Fragment: CORE DOMAIN AND C-TERMINAL DOMAIN 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: TOP1_HUMAN, UniProt: P11387*PLUS, DNA topoisomerase |
#4: Water | ChemComp-HOH / |
Compound details | RESIDUES 215-635 OF CHAIN A COMPRISE THE CORE DOMAIN OF THE MOLECULE. RESIDUES 715-765 OF CHAIN A ...RESIDUES 215-635 OF CHAIN A COMPRISE THE CORE DOMAIN OF THE MOLECULE. RESIDUES 715-765 OF CHAIN A COMPRISE THE C-TERMINAL DOMAIN. 1-22 OF CHAIN C COMPRISE THE SCISSILE STRAND OF THE DNA, 101-122 OF CHAIN D THE INTACT DNA STRAND. NOTE THAT THE LINKER DOMAIN (636-714) IS NOT PRESENT IN THE CONSTRUCT OF THIS RECONSTITU |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.51 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.7 Details: pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 295.00K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 42786 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.7 / % possible all: 95.5 |
Reflection | *PLUS Num. measured all: 79570 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.234 |
-Processing
Software |
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Refinement | Method to determine structure: MIR WITH ANOMALOUS SCATTERING Resolution: 2.1→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.13 Å / Total num. of bins used: 25
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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