[English] 日本語
![](img/lk-miru.gif)
- PDB-7jlj: Crystal structure of Bacillus subtilis UppS in complex with clomiphene -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7jlj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Bacillus subtilis UppS in complex with clomiphene | |||||||||
![]() | Isoprenyl transferase | |||||||||
![]() | TRANSFERASE / undecaprenyl / cis-prenyltransferase / carrier lipid / clomiphene | |||||||||
Function / homology | ![]() di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / Transferases; Transferring alkyl or aryl groups, other than methyl groups / manganese ion binding / magnesium ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Workman, S.D. / Strynadka, N.C.J. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structural Insights into the Inhibition of Undecaprenyl Pyrophosphate Synthase from Gram-Positive Bacteria. Authors: Workman, S.D. / Day, J. / Farha, M.A. / El Zahed, S.S. / Bon, C. / Brown, E.D. / Organ, M.G. / Strynadka, N.C.J. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 63.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 691.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 694.7 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 13.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jliSC ![]() 7jlmC ![]() 7jlrC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 29814.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: uppS, A3772_08985, B4122_2664, B4417_3501, BS16045_01759, ETA10_09020, ETK61_09295, GII79_08795, SC09_Contig19orf01203 Plasmid: pET28a / Production host: ![]() ![]() References: UniProt: A0A063XDJ9, Transferases; Transferring alkyl or aryl groups, other than methyl groups |
---|---|
#2: Chemical | ChemComp-53Q / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.04 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 3000, NaCitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 30, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97952 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→47.41 Å / Num. obs: 5598 / % possible obs: 99.9 % / Redundancy: 9.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.109 / Rrim(I) all: 0.335 / Net I/σ(I): 8 / Num. measured all: 50706 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7JLI Resolution: 3.1→47.41 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.81 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.64 Å2 / Biso mean: 64.8393 Å2 / Biso min: 20.95 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→47.41 Å
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
|