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- PDB-5lb5: Crystal structure of human RECQL5 helicase in complex with ADP/Mg... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5lb5 | ||||||
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Title | Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form). | ||||||
![]() | ATP-dependent DNA helicase Q5 | ||||||
![]() | HYDROLASE / Helicase / RecQ / Transcription / DNA repair / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication / RNA polymerase II complex binding / 3'-5' DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / isomerase activity / helicase activity / replication fork / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / chromosome / mitotic cell cycle / DNA replication / cell division / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Newman, J.A. / Aitkenhead, H. / Savitsky, P. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Gileadi, O. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the RecQ helicase mechanism revealed by the structure of the helicase domain of human RECQL5. Authors: Newman, J.A. / Aitkenhead, H. / Savitsky, P. / Gileadi, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.2 KB | Display | ![]() |
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PDB format | ![]() | 283.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 63.1 KB | Display | |
Data in CIF | ![]() | 87.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lb3C ![]() 5lb8C ![]() 4cdgS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 49537.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 414 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-ADP / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M tris pH 7.5, 23% PEG3350, 0.1M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 2→100.9 Å / Num. obs: 139875 / % possible obs: 99 % / Redundancy: 4.6 % / Biso Wilson estimate: 38.56 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.51 / Mean I/σ(I) obs: 1.5 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CDG Resolution: 2→100.9 Å / Cor.coef. Fo:Fc: 0.9261 / Cor.coef. Fo:Fc free: 0.8953 / SU R Cruickshank DPI: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.192 / SU Rfree Blow DPI: 0.173 / SU Rfree Cruickshank DPI: 0.179
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Displacement parameters | Biso mean: 56.3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.404 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→100.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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