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- PDB-4ugf: 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: 4ugf | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 6-((((3S, 5R)-5-(((6-amino-4-methylpyridin-2-yl)methoxy)methyl) pyrrolidin-3-yl)oxy)methyl)-4-methylpyridin-2-amine | ||||||
![]() | NITRIC OXIDE SYNTHASE OXYGENASE | ||||||
![]() | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / 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 | ![]() | 183.3 KB | Display | ![]() |
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PDB format | ![]() | 142.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ug5C ![]() 4ug6C ![]() 4ug7C ![]() 4ug8C ![]() 4ug9C ![]() 4ugaC ![]() 4ugbC ![]() 4ugcC ![]() 4ugdC ![]() 4ugeC ![]() 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 , 7 types, 334 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/Q16.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/Q16.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/POL.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-Q16 / |
#6: Chemical | ChemComp-GOL / |
#7: Chemical | ChemComp-POL / |
#8: Water | ChemComp-HOH / |
-Details
Sequence details | E25A, E26A, E316A INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % Description: CC ONE HALF FOR FULL DATA SET AT 0.994. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.557 |
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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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→49.58 Å / Num. obs: 45204 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 22.42 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.81→1.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.28 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4D3T Resolution: 1.81→44.057 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
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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: 1.81→44.057 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: 5.4098 Å / Origin y: 19.8146 Å / Origin z: 22.9789 Å
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Refinement TLS group | Selection details: ALL |