+Open data
-Basic information
Entry | Database: PDB / ID: 6dcr | ||||||
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Title | E. coli PriA helicase winged helix domain deletion protein | ||||||
Components | Primosomal protein N' | ||||||
Keywords | DNA BINDING PROTEIN / PriA / Helicase / DNA replication restart | ||||||
Function / homology | Function and homology information DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / 3'-5' DNA helicase activity / replication fork processing / DNA unwinding involved in DNA replication / DNA replication initiation / helicase activity ...DnaB-DnaC-DnaT-PriA-PriC complex / DnaB-DnaC-DnaT-PriA-PriB complex / plasmid maintenance / primosome complex / DNA replication, synthesis of primer / 3'-5' DNA helicase activity / replication fork processing / DNA unwinding involved in DNA replication / DNA replication initiation / helicase activity / response to gamma radiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / double-strand break repair / DNA recombination / DNA replication / hydrolase activity / response to antibiotic / DNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 Å | ||||||
Authors | Satyshur, K.A. / Windgassen, T.A. / Keck, J.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase. Authors: Windgassen, T.A. / Leroux, M. / Satyshur, K.A. / Sandler, S.J. / Keck, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dcr.cif.gz | 704.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dcr.ent.gz | 592.4 KB | Display | PDB format |
PDBx/mmJSON format | 6dcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dc/6dcr ftp://data.pdbj.org/pub/pdb/validation_reports/dc/6dcr | HTTPS FTP |
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-Related structure data
Related structure data | 6dgdC 4nl4S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 77282.500 Da / Num. of mol.: 2 / Mutation: delta 114-174 Source method: isolated from a genetically manipulated source Details: deletion of the winged helix domain (114-174) Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: priA, b3935, JW3906 / Plasmid: pET15b-EcoliPriA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 References: UniProt: P17888, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #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: 2.32 Å3/Da / Density % sol: 46.93 % Description: Thin square sheets. Formed within one day and collected/froze after the second day. |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 50 mM HEPES-HCl pH 7.5, 9.5 % PEG 4000, 4 % Isopropanol, 8 % glycerol, 50 mM sodium malonate, and 25-100 mM sodium fluoride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12712 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12712 Å / Relative weight: 1 |
Reflection | Resolution: 1.978→48.832 Å / Num. obs: 101849 / % possible obs: 96.75 % / Redundancy: 3.7 % / Biso Wilson estimate: 47.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05904 / Rpim(I) all: 0.03598 / Rrim(I) all: 0.06941 / Net I/σ(I): 11.18 |
Reflection shell | Resolution: 1.978→2.049 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.299 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 9857 / CC1/2: 0.374 / Rpim(I) all: 0.7657 / Rrim(I) all: 1.513 / % possible all: 94.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NL4 removing the winged helix domain Resolution: 1.978→48.832 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.978→48.832 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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