[English] 日本語
![](img/lk-miru.gif)
- PDB-2euc: Crystal structure of YfmB from Bacillus subtilis. NESG TARGET SR324 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2euc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of YfmB from Bacillus subtilis. NESG TARGET SR324 | ||||||
![]() | Hypothetical protein yfmB | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG | ||||||
Function / homology | Hypothetical protein YfmB / Protein of unknown function DUF3212 / YfmB domain superfamily / Protein of unknown function (DUF3212) / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YfmB![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Benach, J. / Abashidze, M. / Jayaraman, S. / Janjua, H. / Cooper, B. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal structure of YfmB from bacillus subtilis NESG TARGET SR324. Authors: Benach, J. / Abashidze, M. / Jayaraman, S. / Rong, X. / Acton, T.B. / Montelione, G.T. / Tong, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 45.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 20.3 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: 15309.650 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.31 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 5, 2005 | ||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 22474 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 35.107 | ||||||||||||
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 1.76 / % possible all: 83.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.7618 Å2 / ksol: 0.298453 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→24.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|