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- PDB-5g6q: 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: 5g6q | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 7-(((5-((Methylamino)methyl)pyridin-3-yl)oxy)methyl) quinolin-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: Targeting Bacterial Nitric Oxide Synthase with Aminoquinoline-Based Inhibitors. Authors: Holden, J.K. / Lewis, M.C. / Cinelli, M.A. / Abdullatif, Z. / Pensa, A.V. / 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 | ![]() | 177.7 KB | Display | ![]() |
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PDB format | ![]() | 140.7 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 | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g65C ![]() 5g66C ![]() 5g67C ![]() 5g68C ![]() 5g69C ![]() 5g6aC ![]() 5g6bC ![]() 5g6cC ![]() 5g6dC ![]() 5g6eC ![]() 5g6fC ![]() 5g6gC ![]() 5g6hC ![]() 5g6iC ![]() 5g6jC ![]() 5g6kC ![]() 5g6lC ![]() 5g6mC ![]() 5g6nC ![]() 5g6oC ![]() 5g6pC ![]() 4lwaS 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, 285 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TUE.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H4B.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TUE.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/GOL.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-TUE / | ||
#6: Chemical | ChemComp-BTB / | ||
#7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Sequence details | SURFACE ENTROPY MUTATIONS E25A, E26A AND E316A |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.26 % Description: DATA WAS HIGHLY ANISOTROPIC AND WAS FURTHER SCALED USING THE DIFFRACTION ANISOTROPY SERVER AVAILABLE AT UCLA. CC ONE HALF FOR FULL DATA SET AT 0.997. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.823 |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 31, 2015 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→37.7 Å / Num. obs: 31287 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 20.71 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.03→2.08 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LWA Resolution: 2.03→37.698 Å / SU ML: 0.08 / σ(F): 1.35 / Phase error: 20.2 / Stereochemistry target values: ML Details: RAW DATA HAD STRONG ANISOTROPY AND WAS FURTHER SCALED USING THE DIFFRACTION ANISOTROPY SERVER
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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: 2.03→37.698 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: 5.586 Å / Origin y: 19.6814 Å / Origin z: 22.6023 Å
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Refinement TLS group | Selection details: ALL |