+Open data
-Basic information
Entry | Database: PDB / ID: 3u44 | ||||||
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Title | Crystal structure of AddAB-DNA complex | ||||||
Components |
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Keywords | HYDROLASE/DNA / Helicase / Nuclease / DNA repair / Protein-DNA complex / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information DNA helicase complex / DNA 3'-5' helicase / recombinational repair / 5'-3' exonuclease activity / 3'-5' DNA helicase activity / 3'-5' exonuclease activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / double-stranded DNA binding ...DNA helicase complex / DNA 3'-5' helicase / recombinational repair / 5'-3' exonuclease activity / 3'-5' DNA helicase activity / 3'-5' exonuclease activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / double-stranded DNA binding / 4 iron, 4 sulfur cluster binding / DNA recombination / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.201 Å | ||||||
Authors | Saikrishnan, K. / Krajewski, W. / Wigley, D. | ||||||
Citation | Journal: Embo J. / Year: 2012 Title: Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex. Authors: Saikrishnan, K. / Yeeles, J.T. / Gilhooly, N.S. / Krajewski, W.W. / Dillingham, M.S. / Wigley, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u44.cif.gz | 490.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u44.ent.gz | 387.2 KB | Display | PDB format |
PDBx/mmJSON format | 3u44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u44_validation.pdf.gz | 486.7 KB | Display | wwPDB validaton report |
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Full document | 3u44_full_validation.pdf.gz | 565.1 KB | Display | |
Data in XML | 3u44_validation.xml.gz | 86.3 KB | Display | |
Data in CIF | 3u44_validation.cif.gz | 115 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/3u44 ftp://data.pdbj.org/pub/pdb/validation_reports/u4/3u44 | HTTPS FTP |
-Related 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: 141218.844 Da / Num. of mol.: 1 / Mutation: D1172A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: addA, BSU10630 / Production host: Escherichia coli (E. coli) References: UniProt: P23478, Hydrolases; Acting on ester bonds, DNA helicase |
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#2: Protein | Mass: 134769.406 Da / Num. of mol.: 1 / Mutation: D961A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: addB, BSU10620 / Production host: Escherichia coli (E. coli) References: UniProt: P23477, Hydrolases; Acting on ester bonds, DNA helicase |
#3: DNA chain | Mass: 14716.432 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#4: Chemical | ChemComp-SF4 / |
#5: 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: 2.38 Å3/Da / Density % sol: 48.28 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 15% polyethylene glycol 4000, 0.1M Tris pH 7.5, 0.8 M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009 |
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 45020 / Num. obs: 44552 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 3.2→3.3 Å / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.201→29.884 Å / SU ML: 1 / σ(F): 1.91 / Phase error: 29.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.502 Å2 / ksol: 0.313 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.201→29.884 Å
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Refine LS restraints |
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LS refinement shell |
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