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- PDB-4ug5: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ug5 | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6-(2-(5-(2-(2-amino-6-methylpyridin-4-yl)ethyl)pyridin-3-yl)ethyl)-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: Inhibitor Bound Crystal Structures of Bacterial Nitric Oxide Synthase. Authors: Holden, J.K. / Dejam, D. / Lewis, M.C. / Huang, H. / Kang, S. / Jing, Q. / Xue, F. / Silverman, R.B. / Poulos, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.3 KB | Display | ![]() |
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PDB format | ![]() | 132.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ug6C ![]() 4ug7C ![]() 4ug8C ![]() 4ug9C ![]() 4ugaC ![]() 4ugbC ![]() 4ugcC ![]() 4ugdC ![]() 4ugeC ![]() 4ugfC ![]() 4uggC ![]() 4ughC ![]() 4ugiC ![]() 4ugjC ![]() 4ugkC ![]() 4uglC ![]() 4ugmC ![]() 4ugnC ![]() 4ugoC ![]() 4ugpC ![]() 4ugqC ![]() 4ugrC ![]() 4ugsC ![]() 4ugtC ![]() 4uguC ![]() 4ugvC ![]() 4ugwC ![]() 4ugxC ![]() 4ugyC ![]() 4d3tS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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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.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 51 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/XFK.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/XFK.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-H4B / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-XFK / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.92 % Description: CC ONE HALF FOR FULL DATA SET AT 0.998. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.991 |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2015 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→37.5 Å / Num. obs: 20017 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 15.37 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.35→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4D3T Resolution: 2.352→36.974 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 23.79 / Stereochemistry target values: ML Details: DATA SET WAS HIGHLY ANISOTROPIC SO ONLY 14223 UNIQUE REFLECTIONS WERE USED FOR REFINEMENT.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.352→36.974 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 5.5871 Å / Origin y: 19.8319 Å / Origin z: 21.6555 Å
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Refinement TLS group | Selection details: ALL |