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Yorodumi- PDB-5xg3: Crystal structure of the ATPgS-engaged Smc head domain with an ex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xg3 | ||||||
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Title | Crystal structure of the ATPgS-engaged Smc head domain with an extended coiled coil bound to the C-terminal domain of ScpA derived from Bacillus subtilis | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/CELL CYCLE / Condensin / Smc / ATPase / ScpA / DNA BINDING PROTEIN-CELL CYCLE complex | ||||||
Function / homology | Function and homology information chromosome condensation / sister chromatid cohesion / chromosome segregation / chromosome / DNA replication / cell division / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Shin, H.-C. / Lee, H. / Oh, B.-H. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Structure of Full-Length SMC and Rearrangements Required for Chromosome Organization Authors: Diebold-Durand, M.L. / Lee, H. / Ruiz Avila, L.B. / Noh, H. / Shin, H.C. / Im, H. / Bock, F.P. / Burmann, F. / Durand, A. / Basfeld, A. / Ham, S. / Basquin, J. / Oh, B.-H. / Gruber, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xg3.cif.gz | 173.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xg3.ent.gz | 124.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/5xg3 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/5xg3 | HTTPS FTP |
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-Related structure data
Related structure data | 5nmoC 5nnvC 5xeiC 5xg2C 5xnsC 1xexS C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 49153.883 Da / Num. of mol.: 2 / Fragment: UNP residues 1-219,UNP residues 975-1186 / Mutation: E1118Q,E1118Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: smc, ylqA, BSU15940 / Production host: Escherichia coli (E. coli) / References: UniProt: P51834 #2: Protein | Mass: 10367.890 Da / Num. of mol.: 2 / Fragment: UNP residues 167-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: scpA, SAMN05878487_2386 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1N6WAJ8, UniProt: P35154*PLUS |
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-Non-polymers , 4 types, 8 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CO / | #6: 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: 3.59 Å3/Da / Density % sol: 65.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 3000, 0.1M Imidazole pH8.0, 0.2M LiSO4, 0.05M Hexamine cobalt (III) chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 35074 / % possible obs: 92.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 57.51 Å2 / Net I/σ(I): 12.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XEX Resolution: 3.5→40.989 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.7 / Phase error: 27.08 / 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: 149.68 Å2 / Biso mean: 54.4176 Å2 / Biso min: 3.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.5→40.989 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: 17
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