[English] 日本語
![](img/lk-miru.gif)
- PDB-3dsm: Crystal structure of the surface layer protein BACUNI_02894 from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3dsm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the surface layer protein BACUNI_02894 from Bacteroides uniformis, Northeast Structural Genomics Consortium Target BtR193D. | ||||||
![]() | uncharacterized protein BACUNI_02894 | ||||||
![]() | structural genomics / unknown function / seven_blated beta propeller / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of the surface layer protein BACUNI_02894 from Bacteroides uniformis, Northeast Structural Genomics Consortium Target BtR193D. Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Mao, L. / Janjua, H. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Maglaqui, M. / K Everett, J. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 84.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 67 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 430.3 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38469.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % |
---|---|
Crystal grow | Temperature: 291 K / Method: microbatch under oil / pH: 7 Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100mM Bis-Tris Propane (pH 7), 40% PEG4k, and 100mM NH4Cl , microbatch under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2008 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97909 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 50946 / Num. obs: 42744 / % possible obs: 83.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.05 / Net I/σ(I): 33 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 10.43 / Num. unique all: 5128 / Rsym value: 0.091 / % possible all: 61.7 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.2971 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 18 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→19.47 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
|