[English] 日本語
Yorodumi- PDB-6xk8: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xk8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-((3-((((6-aminopyridin-2-yl)methyl)amino)methyl)phenoxy)methyl)quinolin-2-amine | ||||||
Components | Nitric oxide synthase oxygenase | ||||||
Keywords | OXIDOREDUCTASE/Inhibitor / Inhibitor / Nitric Oxide Synthase / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex | ||||||
Function / homology | Function and homology information nitric-oxide synthase (flavodoxin) / nitric-oxide synthase activity / nitric oxide biosynthetic process / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Lewis, M.C. / Poulos, T.L. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: To Be Published Title: Selective Anti-MRSA inhibitors targeting Nitric Oxide Synthase Authors: Lewis, M.C. / Poulos, T.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6xk8.cif.gz | 114.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6xk8.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xk8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xk8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6xk8_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6xk8_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6xk8_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/6xk8 ftp://data.pdbj.org/pub/pdb/validation_reports/xk/6xk8 | HTTPS FTP |
-Related structure data
Related structure data | 6xcxC 6xk3C 6xk4C 6xk5C 6xk6C 6xk7C 6xmcC 4d3jS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41787.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria) Strain: 168 / Gene: nos, yflM, BSU07630 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O34453, nitric-oxide synthase (flavodoxin) |
---|
-Non-polymers , 7 types, 124 molecules
#2: Chemical | ChemComp-HEM / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-V54 / | ||||||
#4: Chemical | ChemComp-CL / | ||||||
#5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-POL / | #8: 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: 2.83 Å3/Da / Density % sol: 56.55 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Crystallisation conditions: 60 mM BisTris and 40mM citric acid pH 7.6 and 20% vol/vol polyethylene glycol (PEG) 3350, and 1% propanol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→37.56 Å / Num. obs: 23021 / % possible obs: 99.78 % / Redundancy: 2 % / Biso Wilson estimate: 34.23 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 19.62 |
Reflection shell | Resolution: 2.252→2.333 Å / Rmerge(I) obs: 0.05799 / Mean I/σ(I) obs: 8.6 / Num. unique obs: 2234 / CC1/2: 0.995 / % possible all: 99.55 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D3J Resolution: 2.25→37.56 Å / SU ML: 0.1904 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5938 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: 47.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→37.56 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|