[English] 日本語
Yorodumi- PDB-6loi: Crystal structure of Enterococcus faecalis Undecaprenyl pyrophosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6loi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Enterococcus faecalis Undecaprenyl pyrophosphate synthase(EfaUPPS) | ||||||
Components | Isoprenyl transferase | ||||||
Keywords | TRANSFERASE / Isoprenyl transferase | ||||||
Function / homology | Function and homology information Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å | ||||||
Authors | Lin, W. / Wang, C.Y. / Li, W.J. / Wang, F.L. | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Investigations into the Antibacterial Mechanism of Action of Viridicatumtoxins. Authors: Li, W. / Li, L. / Zhang, C. / Cai, Y. / Gao, Q. / Wang, F. / Cao, Y. / Lin, J. / Li, J. / Shang, Z. / Lin, W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6loi.cif.gz | 279.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6loi.ent.gz | 225.1 KB | Display | PDB format |
PDBx/mmJSON format | 6loi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6loi_validation.pdf.gz | 489.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6loi_full_validation.pdf.gz | 512.5 KB | Display | |
Data in XML | 6loi_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 6loi_validation.cif.gz | 65.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/6loi ftp://data.pdbj.org/pub/pdb/validation_reports/lo/6loi | HTTPS FTP |
-Related structure data
Related structure data | 1uehS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33344.656 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) Gene: CYQ15_14590, CYQ44_13430, DAI13_12250, EU507_05085, FKY84_09185 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A246M745, UniProt: Q831K9*PLUS, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M citrate acid/sodium hydroxide (pH 5.0), 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 54407 / % possible obs: 96.5 % / Redundancy: 6.6 % / CC1/2: 0.993 / Net I/σ(I): 1.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1926 / CC1/2: 0.778 / CC star: 0.935 / Rpim(I) all: 0.269 / Rrim(I) all: 0.539 / Rsym value: 0.481 / Χ2: 0.786 / % possible all: 69 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UEH Resolution: 2.503→35.351 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.47 / 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: 154.28 Å2 / Biso mean: 46.5375 Å2 / Biso min: 4.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.503→35.351 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|