[English] 日本語
Yorodumi- PDB-4lwb: Structure of Bacillus subtilis nitric oxide synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lwb | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Bacillus subtilis nitric oxide synthase in complex with 6-((((3R,5S)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl)pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine | ||||||
Components | Nitric oxide synthase oxygenase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE 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 subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Holden, J.K. / Li, H. / Poulos, T.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural and biological studies on bacterial nitric oxide synthase inhibitors. Authors: Holden, J.K. / Li, H. / Jing, Q. / Kang, S. / Richo, J. / Silverman, R.B. / Poulos, T.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lwb.cif.gz | 169.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lwb.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 4lwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lwb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4lwb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4lwb_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 4lwb_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lw/4lwb ftp://data.pdbj.org/pub/pdb/validation_reports/lw/4lwb | HTTPS FTP |
-Related structure data
Related structure data | 4luwC 4luxC 4lwaC 2fbzS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41787.082 Da / Num. of mol.: 1 / Mutation: E25A, E26A, E316A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU07630, nos, yflM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34453, EC: 1.14.13.165 |
---|
-Non-polymers , 6 types, 194 molecules
#2: Chemical | ChemComp-HEM / | ||
---|---|---|---|
#3: Chemical | ChemComp-QJ8 / | ||
#4: Chemical | ChemComp-H4B / | ||
#5: Chemical | ChemComp-CL / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 60 mM Bis-Tris methane, 40 mM citric acid, 20% PEG3350, 1.9% 1-propanol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 26684 / % possible obs: 99.36 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 34.94 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.133 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1327 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FBZ Resolution: 2.15→43.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 10.968 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.182 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 45.431 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→43.9 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|