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- PDB-6loi: Crystal structure of Enterococcus faecalis Undecaprenyl pyrophosp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6loi | ||||||
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Title | Crystal structure of Enterococcus faecalis Undecaprenyl pyrophosphate synthase(EfaUPPS) | ||||||
![]() | Isoprenyl transferase | ||||||
![]() | TRANSFERASE / Isoprenyl transferase | ||||||
Function / homology | ![]() Transferases; Transferring alkyl or aryl groups, other than methyl groups / prenyltransferase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, W. / Wang, C.Y. / Li, W.J. / Wang, F.L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 279.6 KB | Display | ![]() |
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PDB format | ![]() | 225.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.8 KB | Display | ![]() |
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Full document | ![]() | 512.5 KB | Display | |
Data in XML | ![]() | 48.4 KB | Display | |
Data in CIF | ![]() | 65.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uehS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33344.656 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CYQ15_14590, CYQ44_13430, DAI13_12250, EU507_05085, FKY84_09185 Production host: ![]() ![]() References: UniProt: A0A246M745, UniProt: Q831K9*PLUS, Transferases; Transferring alkyl or aryl groups, other than methyl groups #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.79 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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