+
Open data
-
Basic information
Entry | Database: PDB / ID: 5jam | ||||||
---|---|---|---|---|---|---|---|
Title | Yersinia pestis FabV variant T276V | ||||||
![]() | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
![]() | OXIDOREDUCTASE / fatty acid biosynthesis FabV | ||||||
Function / homology | ![]() trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pschibul, A. / Kuper, J. / HIrschbeck, M. / Kisker, C. | ||||||
![]() | ![]() Title: Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia pestis FabV Enoyl-ACP Reductase. Authors: Neckles, C. / Pschibul, A. / Lai, C.T. / Hirschbeck, M. / Kuper, J. / Davoodi, S. / Zou, J. / Liu, N. / Pan, P. / Shah, S. / Daryaee, F. / Bommineni, G.R. / Lai, C. / Simmerling, C. / Kisker, C. / Tonge, P.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 259.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 216 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4bkqC ![]() 4bkrSC ![]() 5g2oC ![]() 5jaiC ![]() 5jaqC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 44201.863 Da / Num. of mol.: 1 / Mutation: T276V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8Z9U1, enoyl-[acyl-carrier-protein] reductase (NADH) | ||
---|---|---|---|
#2: Chemical | ChemComp-NAI / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 150 mM (NH4)2SO4 25-38% PEG 4000 100 mM MES PH 5.6-5.9 PH range: 5.6-5.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2→44.55 Å / Num. obs: 35422 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 10.2 % / Rmerge(I) obs: 1.885 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4bkr Resolution: 2→44.545 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.96
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→44.545 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|