[English] 日本語
![](img/lk-miru.gif)
- PDB-5v1s: Crystal structure of Streptococcus suis SuiB bound to S-adenosylm... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5v1s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Streptococcus suis SuiB bound to S-adenosylmethionine | ||||||
![]() | Radical SAM | ||||||
![]() | METAL BINDING PROTEIN / Radical SAM enzyme / Lys-Trp crosslink / Streptococcus suis / metalloenzyme / SPASM domain / RRE domain | ||||||
Function / homology | ![]() heme biosynthetic process / catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Davis, K.M. / Bacik, J.P. / Ando, N. | ||||||
![]() | ![]() Title: Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. Authors: Davis, K.M. / Schramma, K.R. / Hansen, W.A. / Bacik, J.P. / Khare, S.D. / Seyedsayamdost, M.R. / Ando, N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 184.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 142.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 41 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v1qSC ![]() 5v1tC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53044.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop Details: A solution containing 18.9 mg/mL His6-tagged SuiB in in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed 1:1 with precipitant solution. Small ...Details: A solution containing 18.9 mg/mL His6-tagged SuiB in in storage buffer [100 mM HEPES, pH 7.5, 300 mM KCl, 5 mM DTT, 10% (v/v) glycerol] was mixed 1:1 with precipitant solution. Small clusters of crystals were formed within 24 hrs. A seed stock was then produced by combining a single sitting well with 10 uL of reservoir solution and 10 uL of enzyme at 8 mg/mL, followed by brief vortexing. Following seeding, a resulting crystal was incubated in precipitant solution containing ~6 mM SAM for 30 min prior to transfer to cryosolution.The precipitant solution was 100 mM MES, pH 6.0, 15% (w/v) PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→29.47 Å / Num. obs: 38407 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.49→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2 / Num. unique all: 4234 / % possible all: 99 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5V1Q Resolution: 2.492→29.47 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.08
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.492→29.47 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|