+
Open data
-
Basic information
Entry | Database: PDB / ID: 1kzf | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Acyl-homoserine Lactone Synthase, EsaI | ||||||
![]() | acyl-homoserinelactone synthase EsaI | ||||||
![]() | LIGASE / alpha-beta / autoinducer synthase / acylhomoserine lactone / quorum sensing / bacterial pathogenesis | ||||||
Function / homology | ![]() acyl-homoserine-lactone synthase / N-acyl homoserine lactone synthase activity / quorum sensing / signal transduction Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watson, W.T. / Minogue, T.D. / Val, D.L. / Beck von Bodman, S. / Churchill, M.E.A. | ||||||
![]() | ![]() Title: Structural basis and specificity of acyl-homoserine lactone signal production in bacterial quorum sensing. Authors: Watson, W.T. / Minogue, T.D. / Val, D.L. / von Bodman, S.B. / Churchill, M.E. #1: ![]() Title: Crystallization and Rhenium MAD Phasing of the Acyl-homoserinelactone Synthase EsaI Authors: Watson, W.T. / Murphy IV, F.V. / Gould, T.A. / Jambeck, P. / Val, D.L. / Cronan JR., J.E. / Beck von Bodman, S. / Churchill, M.E.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 54.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 368 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 370.6 KB | Display | |
Data in XML | ![]() | 5.6 KB | Display | |
Data in CIF | ![]() | 8.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k4jSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26040.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Pantoea stewartii / Strain: subsp. stewartii / Gene: EsaI/EsaR gene cluster / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.25 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: MES, PEG 4000, 2-propanol, EDTA, NaN3, 2-mercaptoethanol, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2000 |
Radiation | Monochromator: CARS-designed Si(111) double-bounce monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→99 Å / Num. all: 19521 / Num. obs: 19521 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 28.553 Å2 / Rsym value: 0.039 / Net I/σ(I): 48.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 1799 / Rsym value: 0.195 / % possible all: 92 |
Reflection | *PLUS Lowest resolution: 99 Å / Num. measured all: 174794 / Rmerge(I) obs: 0.039 |
Reflection shell | *PLUS % possible obs: 92 % / Rmerge(I) obs: 0.195 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K4J Resolution: 1.8→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.4 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.017
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 9.5 % / Rfactor all: 0.224 / Rfactor obs: 0.209 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.209 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
| |||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.86 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.251 / Rfactor obs: 0.251 |