+Open data
-Basic information
Entry | Database: PDB / ID: 7lgb | ||||||
---|---|---|---|---|---|---|---|
Title | ChsB1 in complex with NAD+ | ||||||
Components | 3-ketoacyl-ACP reductase | ||||||
Keywords | OXIDOREDUCTASE / short-chain type alcohol dehydrogenase/reductase hydroxyacyl-CoA dehydrogenase | ||||||
Function / homology | Function and homology information 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Yuan, T. / Werman, J.M. / Yin, X. / Yang, M. / Garcia-Diaz, M. / Sampson, N.S. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acs Infect Dis. / Year: 2021 Title: Enzymatic beta-Oxidation of the Cholesterol Side Chain in Mycobacterium tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-cholest-4,22-dien-24-oyl-CoA. Authors: Yuan, T. / Werman, J.M. / Yin, X. / Yang, M. / Garcia-Diaz, M. / Sampson, N.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7lgb.cif.gz | 76.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7lgb.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 7lgb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lgb_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7lgb_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7lgb_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7lgb_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/7lgb ftp://data.pdbj.org/pub/pdb/validation_reports/lg/7lgb | HTTPS FTP |
-Related structure data
Related structure data | 7lg9C 4kzpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32764.697 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: fabG_8, fabG_1, fabG_2, fabG_4, fabG_6, fabG_7, DSI38_08445, E5M52_16205, ERS007665_00489, ERS007670_00458, ERS007679_00994, ERS007681_00640, ERS007741_01258, ERS013471_03025, ERS023446_03243, ...Gene: fabG_8, fabG_1, fabG_2, fabG_4, fabG_6, fabG_7, DSI38_08445, E5M52_16205, ERS007665_00489, ERS007670_00458, ERS007679_00994, ERS007681_00640, ERS007741_01258, ERS013471_03025, ERS023446_03243, ERS024276_00059, ERS075361_03673, F6W99_02176, FRD82_16680, SAMEA2683035_03264 Production host: Rhodococcus jostii RHA1 (bacteria) References: UniProt: A0A045J1S8, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, 3-oxoacyl-[acyl-carrier-protein] reductase |
---|---|
#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
---|---|
Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium citrate, 0.1M HEPES pH7.5, 30% v/v 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→42.48 Å / Num. obs: 103397 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.24 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.21→2.25 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 103397 / CC1/2: 0.739 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KZP Resolution: 2.21→42.48 Å / SU ML: 0.2271 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.7343 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→42.48 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|