+Open data
-Basic information
Entry | Database: PDB / ID: 6iub | ||||||
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Title | Structure of Helicobacter pylori Soj protein | ||||||
Components | SpoOJ regulator (Soj) | ||||||
Keywords | DNA BINDING PROTEIN / Partition protein | ||||||
Function / homology | Function and homology information CobQ/CobB/MinD/ParA nucleotide binding domain / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 Å | ||||||
Authors | Chu, C.H. / Yen, C.Y. / Sun, Y.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Crystal structures of HpSoj-DNA complexes and the nucleoid-adaptor complex formation in chromosome segregation. Authors: Chu, C.H. / Yen, C.Y. / Chen, B.W. / Lin, M.G. / Wang, L.H. / Tang, K.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 | 6iub.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iub.ent.gz | 97.9 KB | Display | PDB format |
PDBx/mmJSON format | 6iub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/6iub ftp://data.pdbj.org/pub/pdb/validation_reports/iu/6iub | HTTPS FTP |
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-Related structure data
Related structure data | 6iucC 6iudC 2bekS 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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Unit cell |
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-Components
#1: Protein | Mass: 30608.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria) Strain: ATCC 700392 / 26695 / Gene: HP_1139 / Production host: Escherichia coli (E. coli) / References: UniProt: O25759 #2: Chemical | #3: Chemical | #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: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: Bicine (pH 9.0), Tacsimate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Jan 21, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 37426 / % possible obs: 93.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 19.23 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 3776 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BEK Resolution: 1.902→29.951 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.42 Å2 / Biso mean: 21.9 Å2 / Biso min: 5.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.902→29.951 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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