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Yorodumi- PDB-1rrj: Structural Mechanisms of Camptothecin Resistance by Mutations in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rrj | ||||||
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Title | Structural Mechanisms of Camptothecin Resistance by Mutations in Human Topoisomerase I | ||||||
Components |
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Keywords | ISOMERASE/DNA / human topoisomerase I / topotecan / camptothecin / 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: 2.3 Å | ||||||
Authors | Chrencik, J.E. / Staker, B.L. / Burgin, A.B. / Stewart, L. / Redinbo, M.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Mechanisms of camptothecin resistance by human topoisomerase I mutations Authors: Chrencik, J.E. / Staker, B.L. / Burgin, A.B. / Pourquier, P. / 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 | 1rrj.cif.gz | 169.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rrj.ent.gz | 126.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rrj_validation.pdf.gz | 530.8 KB | Display | wwPDB validaton report |
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Full document | 1rrj_full_validation.pdf.gz | 545.5 KB | Display | |
Data in XML | 1rrj_validation.xml.gz | 15 KB | Display | |
Data in CIF | 1rrj_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/1rrj ftp://data.pdbj.org/pub/pdb/validation_reports/rr/1rrj | HTTPS FTP |
-Related structure data
Related structure data | 1rr8C 1k4tS S: Starting model for refinement C: citing same article (ref.) |
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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
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 6806.467 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 |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 66964.148 Da / Num. of mol.: 1 / Mutation: Asn722Ser Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TOP1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11387, DNA topoisomerase |
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-Non-polymers , 3 types, 438 molecules
#4: Chemical | ChemComp-TTG / |
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#5: Chemical | ChemComp-TTC / ( |
#6: 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: 3.06 Å3/Da / Density % sol: 59.85 % | ||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, 200mM lithium sulfate, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2003 / Details: mirrors |
Radiation | Monochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→43.69 Å / Num. all: 113083 / Num. obs: 56412 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.3 Å2 |
Reflection shell | Resolution: 2.3→2.44 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1K4T Resolution: 2.3→43.69 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→43.69 Å
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Refine LS restraints |
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