[English] 日本語
![](img/lk-miru.gif)
- PDB-2heu: Atomic resolution structure of apo-form of RafE from Streptococcu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2heu | ||||||
---|---|---|---|---|---|---|---|
Title | Atomic resolution structure of apo-form of RafE from Streptococcus pneumoniae | ||||||
![]() | Sugar ABC transporter, sugar-binding protein | ||||||
![]() | TRANSPORT PROTEIN / Periplasmic binding protein | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Paterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W. | ||||||
![]() | ![]() Title: High resolution crystal structures of RafE from Streptococcus pneumoniae. Authors: Paterson, N.G. / Riboldi-Tunnicliffe, A. / Mitchell, T.J. / Isaacs, N.W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 616.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 510.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 513.3 KB | Display | |
Data in XML | ![]() | 74.7 KB | Display | |
Data in CIF | ![]() | 120.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
3 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | Biological subunit is monomeric |
-
Components
#1: Protein | Mass: 45136.852 Da / Num. of mol.: 3 / Fragment: Residues 33-415 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-TRS / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.96 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% (w/v) PEG 4000, 0.1M Tris.HCl, 0.05M CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→19.82 Å / Num. all: 543433 / Num. obs: 543433 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.12 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.062 / Χ2: 0.97 / Net I/σ(I): 9.8 / Scaling rejects: 16905 |
Reflection shell | Resolution: 1.04→1.08 Å / Redundancy: 3.09 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.7 / Num. measured all: 162181 / Num. unique all: 52441 / Χ2: 1.05 / % possible all: 94.2 |
-Phasing
Phasing MR |
|
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.116 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.04→19.82 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.04→1.067 Å / Total num. of bins used: 20
|