+Open data
-Basic information
Entry | Database: PDB / ID: 4nl8 | ||||||
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Title | PriA Helicase Bound to SSB C-terminal Tail Peptide | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / PriA / SSB C-Terminal peptide / RecA fold / winged helix domain / helicase | ||||||
Function / homology | Function and homology information primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / DNA replication / DNA recombination / hydrolase activity / DNA repair ...primosome complex / DNA replication, synthesis of primer / DNA unwinding involved in DNA replication / DNA helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / single-stranded DNA binding / DNA replication / DNA recombination / hydrolase activity / DNA repair / DNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.08 Å | ||||||
Authors | Bhattacharyya, B. / George, N.P. / Thurmes, T.M. / Keck, J.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Structural mechanisms of PriA-mediated DNA replication restart. Authors: Bhattacharyya, B. / George, N.P. / Thurmes, T.M. / Zhou, R. / Jani, N. / Wessel, S.R. / Sandler, S.J. / Ha, T. / 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 | 4nl8.cif.gz | 347.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nl8.ent.gz | 279.4 KB | Display | PDB format |
PDBx/mmJSON format | 4nl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4nl8_validation.pdf.gz | 482.3 KB | Display | wwPDB validaton report |
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Full document | 4nl8_full_validation.pdf.gz | 508.3 KB | Display | |
Data in XML | 4nl8_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 4nl8_validation.cif.gz | 79 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/4nl8 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/4nl8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 3 - 731 / Label seq-ID: 19 - 747
NCS ensembles :
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-Components
#1: Protein/peptide | Mass: 1300.392 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: HS11286 / Gene: KPHS_02830, ssb c-terminal peptide / Production host: Escherichia coli (E. coli) / References: UniProt: G8W6B0, UniProt: A0A0H3GL04*PLUS #2: Protein | Mass: 83237.211 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria) Strain: MGH 78578 / Gene: KPN78578_41850, KPN_04230, priA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: A6TGC5 #3: Chemical | ChemComp-ZN / |
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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: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M ammonium acetate, 0.015 M magnesium acetate tetrahydrate, 0.05 M sodium cacodylate trihydrate pH 6.5, and 10% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2013 / Details: C(111) |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 4.08→50 Å / Num. obs: 21752 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.108 / Net I/σ(I): 10.91 |
Reflection shell | Resolution: 4.08→4.17 Å / Mean I/σ(I) obs: 1.89 / Rsym value: 0.495 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.08→50 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.867 / SU B: 58.968 / SU ML: 0.776 / Cross valid method: THROUGHOUT / ESU R Free: 1.055 / 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: 142.274 Å2
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Refinement step | Cycle: LAST / Resolution: 4.08→50 Å
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Refine LS restraints |
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