[English] 日本語
![](img/lk-miru.gif)
- PDB-6vhv: Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vhv | ||||||
---|---|---|---|---|---|---|---|
Title | Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN | ||||||
![]() | NpsA Adenylation Domain | ||||||
![]() | BIOSYNTHETIC PROTEIN / adenylation / tilivalline / tilimycin / NRPS / nonribosomal peptide synthetase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kreitler, D.F. / Gulick, A.M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic PathogenKlebsiella oxytoca. Authors: Alexander, E.M. / Kreitler, D.F. / Guidolin, V. / Hurben, A.K. / Drake, E. / Villalta, P.W. / Balbo, S. / Gulick, A.M. / Aldrich, C.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 197.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 140.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6vhtC ![]() 6vhuSC ![]() 6vhwC ![]() 6vhxC ![]() 6vhyC ![]() 6vhzC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 55554.848 Da / Num. of mol.: 1 / Mutation: E312A, E313A, Q314A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-QXG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
---|---|
Crystal grow | Temperature: 296 K / Method: microbatch / pH: 6.6 Details: well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0. ...Details: well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5 mM 3HA-AMSN droplet: 2 uL protein solution, 1 uL well solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→68.1 Å / Num. obs: 12516 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 86.74 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Rsym value: 0.149 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.89→2.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 605 / CC1/2: 0.412 / Rpim(I) all: 0.858 / Rrim(I) all: 2.261 / Rsym value: 2.088 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6vhu Resolution: 2.89→68.1 Å / SU ML: 0.508 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.174
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→68.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|