+
Open data
-
Basic information
Entry | Database: PDB / ID: 3u6y | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ALBA2-DNA complex | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / ALBA 2 / Archaea / DNA-Binding Protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / DNA Binding Protein-DNA complex | ||||||
Function / homology | ![]() chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kumarevel, T. / Tanaka, T. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Crystal structure of archaeal chromatin protein Alba2-double-stranded DNA complex from Aeropyrum pernix K1. Authors: Tanaka, T. / Padavattan, S. / Kumarevel, T. #1: Journal: Proteins / Year: 2008 Title: Crystal structure of an archaeal specific DNA-binding protein (Ape10b2) from Aeropyrum pernix K1. Authors: Kumarevel, T. / Sakamoto, K. / Gopinath, S.C. / Shinkai, A. / Kumar, P.K. / Yokoyama, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 43.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2h9uS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11397.197 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: DNA chain | | Mass: 1481.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | | Mass: 1521.024 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.2M AMMONIUM DIHYDROGEN PHOSPHATE, PEG 3350, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 3, 2009 / Details: SI II CHANNEL |
Radiation | Monochromator: SI II CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. all: 15617 / Num. obs: 15617 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 14.1 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.496 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2H9U Resolution: 2→19.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1188968 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.36 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.03 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.93 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|