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Yorodumi- PDB-7dwr: Structure of Sulfolobus solfataricus SegA-ADP complex bound to DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dwr | ||||||
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Title | Structure of Sulfolobus solfataricus SegA-ADP complex bound to DNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / PARTITION PROTEIN / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / SOJ protein (Soj) Function and homology information | ||||||
Biological species | Saccharolobus solfataricus (archaea) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Yen, C.Y. / Lin, M.G. / Hsiao, C.D. / Sun, Y.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Chromosome segregation in Archaea: SegA- and SegB-DNA complex structures provide insights into segrosome assembly. Authors: Yen, C.Y. / Lin, M.G. / Chen, B.W. / Ng, I.W. / Read, N. / Kabli, A.F. / Wu, C.T. / Shen, Y.Y. / Chen, C.H. / Barilla, D. / Sun, Y.J. / Hsiao, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dwr.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dwr.ent.gz | 183.1 KB | Display | PDB format |
PDBx/mmJSON format | 7dwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/7dwr ftp://data.pdbj.org/pub/pdb/validation_reports/dw/7dwr | HTTPS FTP |
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-Related structure data
Related structure data | 7dutSC 7duvC 7dv2C 7dv3C 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 24324.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: soj, SSO0034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q981B3 |
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-DNA chain , 2 types, 4 molecules EGFH
#2: DNA chain | Mass: 7483.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 7256.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 31 molecules
#4: Chemical | ChemComp-ADP / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: MES sodium salt pH 6.5, PEG8000, calcium acetate. |
-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: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 7, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. obs: 32772 / % possible obs: 94.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.066 / Rrim(I) all: 0.127 / Χ2: 0.92 / Net I/σ(I): 6.9 / Num. measured all: 117429 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DUT Resolution: 2.8→27.68 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.81 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.75 Å2 / Biso mean: 58.5863 Å2 / Biso min: 19.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→27.68 Å
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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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