[English] 日本語
Yorodumi- PDB-8crl: Crystal structure of LplA1 in complex with the inhibitor C3 (List... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8crl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LplA1 in complex with the inhibitor C3 (Listeria monocytogenes) | ||||||
Components | lipoate--protein ligase | ||||||
Keywords | LIGASE / LIPOATE / SALVAGE / ANTI-INFECTIVES / DRUG DEVELOPMENT / INHIBITOR | ||||||
Function / homology | Function and homology information lipoyltransferase activity / lipoate-protein ligase activity / lipoate-protein ligase / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Listeria monocytogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Dienemann, J.-N. / Chen, S.-Y. / Hitzenberger, M. / Sievert, M.L. / Hacker, S.M. / Prigge, S.T. / Zacharias, M. / Groll, M. / Sieber, S.A. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: A Chemical Proteomic Strategy Reveals Inhibitors of Lipoate Salvage in Bacteria and Parasites. Authors: Dienemann, J.N. / Chen, S.Y. / Hitzenberger, M. / Sievert, M.L. / Hacker, S.M. / Prigge, S.T. / Zacharias, M. / Groll, M. / Sieber, S.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8crl.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8crl.ent.gz | 197.6 KB | Display | PDB format |
PDBx/mmJSON format | 8crl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8crl_validation.pdf.gz | 804.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8crl_full_validation.pdf.gz | 812.9 KB | Display | |
Data in XML | 8crl_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 8crl_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/8crl ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8crl | HTTPS FTP |
-Related structure data
Related structure data | 8criSC 8crjC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 38419.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) Gene: AF817_03905, AF817_17765, APD94_04200, APD94_16795, D4271_05835, D4271_17085, D4C60_07100, D4C60_17245, D4D89_06525, D4D89_17125, D4U23_01750, D4U23_16900, E0I39_06590, E0I39_16500, E1V33_ ...Gene: AF817_03905, AF817_17765, APD94_04200, APD94_16795, D4271_05835, D4271_17085, D4C60_07100, D4C60_17245, D4D89_06525, D4D89_17125, D4U23_01750, D4U23_16900, E0I39_06590, E0I39_16500, E1V33_06915, E1W43_02450, E1W43_16025, FJU19_06430, FJU19_16220, FORC68_0962, G3R95_001339, G3R95_003435, GON91_05790, GT011_03885, GT011_16715, GXB45_04655, GXB45_16710, GYP27_11270, GYP27_15895, GYU24_04270, GYU24_17075 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D2IX29, lipoate-protein ligase |
---|
-Non-polymers , 5 types, 27 molecules
#2: Chemical | ChemComp-VK9 / ~{ | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.27 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS, 0.2 M CaCl2, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 23850 / % possible obs: 96.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2622 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8CRI Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.915 / SU B: 36.348 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.491 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|