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Yorodumi- PDB-5h69: Crystal structure of an asymmetric dimer of the Geobacillus stear... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h69 | ||||||
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Title | Crystal structure of an asymmetric dimer of the Geobacillus stearothermophilus SMC hinge domain | ||||||
Components | Chromosome partition protein Smc | ||||||
Keywords | DNA BINDING PROTEIN / CELL CYCLE / SMC protein | ||||||
Function / homology | Function and homology information sister chromatid cohesion / chromosome condensation / chromosome / DNA replication / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus 10 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20040022156 Å | ||||||
Authors | Kamada, K. / Hirano, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Structure / Year: 2017 Title: Overall Shapes of the SMC-ScpAB Complex Are Determined by Balance between Constraint and Relaxation of Its Structural Parts Authors: Kamada, K. / Su'etsugu, M. / Takada, H. / Miyata, M. / Hirano, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h69.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h69.ent.gz | 85.1 KB | Display | PDB format |
PDBx/mmJSON format | 5h69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h6/5h69 ftp://data.pdbj.org/pub/pdb/validation_reports/h6/5h69 | HTTPS FTP |
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-Related structure data
Related structure data | 5h66C 5h67C 5h68C 1gxjS 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
#1: Protein | Mass: 28967.014 Da / Num. of mol.: 2 / Fragment: UNP residues 463-719 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus 10 (bacteria) Gene: smc, GT50_02560 / Plasmid: pET-28m / Details (production host): modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0K2H586 #2: 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: 3.08 Å3/Da / Density % sol: 60.07 % / Description: Needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M magnesium formate, 15%(w/v) PEG 33500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2012 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 34064 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 30.89 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/av σ(I): 46.9 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.214 / Rsym value: 0.214 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GXJ Resolution: 2.20040022156→36.5631717256 Å / SU ML: 0.226772278776 / Cross valid method: FREE R-VALUE / σ(F): 1.38098488499 / Phase error: 24.9111737956
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5138348812 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.20040022156→36.5631717256 Å
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Refine LS restraints |
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LS refinement shell |
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