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Yorodumi- PDB-1lpq: Human DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lpq | ||||||
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Title | Human DNA Topoisomerase I (70 Kda) In Non-Covalent Complex With A 22 Base Pair DNA Duplex Containing an 8-oxoG Lesion | ||||||
Components |
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Keywords | ISOMERASE/DNA / protein-DNA complex / DNA damage / induced conformational change / 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: 3.14 Å | ||||||
Authors | Lesher, D.T. / Pommier, Y. / Stewart, L. / Redinbo, M.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: 8-Oxoguanine rearranges the active site of human topoisomerase I Authors: Lesher, D.T. / Pommier, Y. / Stewart, L. / Redinbo, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpq.cif.gz | 152.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpq.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpq ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpq | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 6822.467 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6690.362 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 66767.062 Da / Num. of mol.: 1 / Mutation: Y723F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.32 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: Tris-HCl, MES, PEG 400, Magnesium chloride, dithiothreitol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / Details: Stewart, L., (1998) Science, 279, 1534. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12B / Wavelength: 1.1 |
Detector | Type: BRANDEIS / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.14→20 Å / Num. obs: 17165 / % possible obs: 95.6 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 2.5 % / Rmerge(I) obs: 0.334 / Rsym value: 0.2 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 3.14→3.19 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.265 / % possible all: 90.5 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 2.22 % / Num. measured all: 38120 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 90.5 % / Rmerge(I) obs: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→19.87 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 1588348.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 64.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.14→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.14→3.34 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.258 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.391 / Rfactor Rwork: 0.36 |