[English] 日本語
![](img/lk-miru.gif)
- PDB-5h69: Crystal structure of an asymmetric dimer of the Geobacillus stear... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5h69 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an asymmetric dimer of the Geobacillus stearothermophilus SMC hinge domain | ||||||
![]() | Chromosome partition protein Smc | ||||||
![]() | DNA BINDING PROTEIN / CELL CYCLE / SMC protein | ||||||
Function / homology | ![]() sister chromatid cohesion / chromosome condensation / chromosome / DNA replication / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kamada, K. / Hirano, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 135.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.6 KB | Display | |
Data in XML | ![]() | 20.2 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5h66C ![]() 5h67C ![]() 5h68C ![]() 1gxjS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
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.) ![]() ![]() Gene: smc, GT50_02560 / Plasmid: pET-28m / Details (production host): modified / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % / Description: Needle |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|