+Open data
-Basic information
Entry | Database: PDB / ID: 8jmk | ||||||
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Title | Structure of Helicobacter pylori Soj mutant, D41A bound to DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Helicobacter pylori / chromosome partition | ||||||
Function / homology | AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / metal ion binding / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / SpoOJ regulator (Soj) Function and homology information | ||||||
Biological species | Helicobacter pylori 26695 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Wu, C.T. / Chu, C.H. / Sun, Y.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Insights into the molecular mechanism of ParABS system in chromosome partition by HpParA and HpParB. Authors: Chu, C.H. / Wu, C.T. / Lin, M.G. / Yen, C.Y. / Wu, Y.Z. / Hsiao, C.D. / Sun, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jmk.cif.gz | 478.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jmk.ent.gz | 391.8 KB | Display | PDB format |
PDBx/mmJSON format | 8jmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jmk_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8jmk_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8jmk_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 8jmk_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/8jmk ftp://data.pdbj.org/pub/pdb/validation_reports/jm/8jmk | HTTPS FTP |
-Related structure data
Related structure data | 8jmjC 8jmlC 6iucS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29158.982 Da / Num. of mol.: 4 / Mutation: D41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1139 / Production host: Escherichia coli (E. coli) / References: UniProt: O25759 #2: DNA chain | | Mass: 7256.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 7483.842 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-MG / Has ligand of interest | N | |
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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: 2.98 Å3/Da / Density % sol: 58.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 25% Ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→30 Å / Num. obs: 44627 / % possible obs: 96.4 % / Redundancy: 1.9 % / CC1/2: 0.756 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IUC Resolution: 2.7→27.879 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 35.67 / 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: 2.7→27.879 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 35.0209 Å / Origin y: -31.7739 Å / Origin z: 70.5936 Å
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Refinement TLS group | Selection details: all |