[English] 日本語
![](img/lk-miru.gif)
- PDB-4d3o: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4d3o | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6-(3-(2-(1H-Pyrrolo(2,3-b)pyridin-6-yl)ethyl)-5-(aminomethyl) phenethyl)-4-methylpyridin-2-amine | ||||||
![]() | NITRIC OXIDE SYNTHASE OXYGENASE | ||||||
![]() | OXIDOREDUCTASE / INHIBITOR | ||||||
Function / homology | ![]() nitric-oxide synthase (flavodoxin) / nitric-oxide synthase activity / nitric oxide biosynthetic process / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Holden, J.K. / Poulos, T.L. | ||||||
![]() | ![]() Title: Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors. Authors: Holden, J.K. / Kang, S. / Hollingsworth, S.A. / Li, H. / Lim, N. / Chen, S. / Huang, H. / Xue, F. / Tang, W. / Silverman, R.B. / Poulos, T.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 180.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 142 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 28.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d3iC ![]() 4d3jC ![]() 4d3kC ![]() 4d3mC ![]() 4d3nC ![]() 4d3tC ![]() 4d3uC ![]() 4d3vC ![]() 4lwaS C: citing same article ( S: Starting model for refinement |
---|---|
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 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 328 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/S97.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/S97.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / | ||
---|---|---|---|
#3: Chemical | ChemComp-CL / | ||
#4: Chemical | ChemComp-S97 / | ||
#5: Chemical | ChemComp-POL / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.91 % Description: CC ONE HALF FOR FULL DATASET AT 0.991 CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.868 |
---|---|
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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999978 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.21 Å / Num. obs: 37512 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 19.18 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 95.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LWA Resolution: 1.9→46.727 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 20.96 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.727 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 5.6999 Å / Origin y: 19.4395 Å / Origin z: 23.0168 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |