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Yorodumi- PDB-6kcs: Crystal structure of HIRAN domain of HLTF in complex with duplex DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kcs | ||||||||||||
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Title | Crystal structure of HIRAN domain of HLTF in complex with duplex DNA | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | Function and homology information hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / mRNA transcription by RNA polymerase II / RING-type E3 ubiquitin transferase / nuclear matrix / RNA polymerase II transcription regulator complex ...hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / regulation of neurogenesis / ATP-dependent activity, acting on DNA / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / mRNA transcription by RNA polymerase II / RING-type E3 ubiquitin transferase / nuclear matrix / RNA polymerase II transcription regulator complex / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / protein ubiquitination / DNA repair / ubiquitin protein ligase binding / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / zinc ion binding / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Hishiki, A. / Hashimoto, A. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biochem. / Year: 2020 Title: Structure of HIRAN domain of human HLTF bound to duplex DNA provides structural basis for DNA unwinding to initiate replication fork regression. Authors: Hishiki, A. / Sato, M. / Hashimoto, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kcs.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kcs.ent.gz | 53.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/6kcs ftp://data.pdbj.org/pub/pdb/validation_reports/kc/6kcs | HTTPS FTP |
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-Related structure data
Related structure data | 4xzfS S: Starting model for refinement |
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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: Protein | Mass: 13350.282 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLTF, HIP116A, RNF80, SMARCA3, SNF2L3, ZBU1 / Production host: Escherichia coli (E. coli) References: UniProt: Q14527, RING-type E3 ubiquitin transferase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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#2: DNA chain | Mass: 4279.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: 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: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 27, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 9284 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.1→2.21 Å / Rmerge(I) obs: 0.605 / Num. unique obs: 1336 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xzf Resolution: 2.1→19.95 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 14.156 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.209
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.363 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→19.95 Å
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Refine LS restraints |
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