+Open data
-Basic information
Entry | Database: PDB / ID: 5mkw | ||||||
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Title | Crystal structure of the human ZRANB3 HNH domain | ||||||
Components | DNA annealing helicase and endonuclease ZRANB3 | ||||||
Keywords | HYDROLASE / endonuclease / metalloprotein / zinc-binding / DNA-binding | ||||||
Function / homology | Function and homology information DNA rewinding / negative regulation of DNA recombination / replication fork reversal / ATP-dependent DNA/DNA annealing activity / ATP-dependent chromatin remodeler activity / K63-linked polyubiquitin modification-dependent protein binding / replication fork processing / nuclear replication fork / response to UV / DNA endonuclease activity ...DNA rewinding / negative regulation of DNA recombination / replication fork reversal / ATP-dependent DNA/DNA annealing activity / ATP-dependent chromatin remodeler activity / K63-linked polyubiquitin modification-dependent protein binding / replication fork processing / nuclear replication fork / response to UV / DNA endonuclease activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Hydrolases; Acting on ester bonds / DNA repair / DNA damage response / zinc ion binding / nucleoplasm / ATP binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ariza, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural insights into the function of ZRANB3 in replication stress response. Authors: Sebesta, M. / Cooper, C.D.O. / Ariza, A. / Carnie, C.J. / Ahel, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mkw.cif.gz | 112.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mkw.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 5mkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/5mkw ftp://data.pdbj.org/pub/pdb/validation_reports/mk/5mkw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 14009.960 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZRANB3 / Production host: Escherichia coli (E. coli) References: UniProt: Q5FWF4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Hydrolases; Acting on ester bonds #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG10,000 + 100 mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 2→54.88 Å / Num. obs: 24666 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.208 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.862 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.522 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: obtained by SeMet SAD phasing Resolution: 2→54.48 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 7.235 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.134 Å2
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Refinement step | Cycle: 1 / Resolution: 2→54.48 Å
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Refine LS restraints |
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