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- PDB-4d3k: 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: 4d3k | ||||||
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Title | Structure of Bacillus subtilis nitric oxide synthase in complex with 6,6'-((5-(3-aminopropyl)-1,3-phenylene)bis(ethane-2,1-diyl))bis(4- methylpyridin-2-amine) | ||||||
![]() | NITRIC OXIDE SYNTHASE OXYGENASE | ||||||
![]() | OXIDOREDUCTASE / NITRIC / NITRIC OXIDE SYNTHASE | ||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 335.4 KB | Display | ![]() |
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PDB format | ![]() | 273.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 35.4 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d3iC ![]() 4d3jC ![]() 4d3mC ![]() 4d3nC ![]() 4d3oC ![]() 4d3tC ![]() 4d3uC ![]() 4d3vC ![]() 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41787.082 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 709 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/12S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/12S.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.08 % Description: CC ONE HALF FOR FULL DATASET WAS 0.999 AND FOR HIGHEST SHELL WAS 0.990 |
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Crystal grow | pH: 7.6 / Details: pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→49.51 Å / Num. obs: 63764 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 20.33 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2.02→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 8.5 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LWA Resolution: 2.017→75.435 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 23.57 / 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: 2.017→75.435 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: 14.8783 Å / Origin y: -0.0516 Å / Origin z: -8.4516 Å
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Refinement TLS group | Selection details: ALL |