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- PDB-4d3t: 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: 4d3t | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N-{3-[(1S)-2-(3-{(Z)-[amino(thiophen-2-yl)methylidene]amino}phenoxy)-1-hydroxyethyl]phenyl}thiophene-2-carboximidamide | ||||||
![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.4 KB | Display | ![]() |
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PDB format | ![]() | 143.3 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 | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4d3iC ![]() 4d3jC ![]() 4d3kC ![]() 4d3mC ![]() 4d3nC ![]() 4d3oC ![]() 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 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.) ![]() ![]() Production host: ![]() ![]() |
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-Non-polymers , 6 types, 319 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/RFQ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/POL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/RFQ.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-CL / | ||||
#4: Chemical | ChemComp-RFQ / | ||||
#5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Sequence details | MUTATIONS E25A, E26A, AND E316A INTRODUCED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.15 % Description: CC ONE HALF FOR FULL DATA SET AT 0.999 CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.601 RMERGE FOR HIGH RESOLUTION SHELL AT 2.151 |
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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→37.02 Å / Num. obs: 69172 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.57 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 0.7 / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4LWA Resolution: 1.55→37.025 Å / SU ML: 0.17 / σ(F): 1.33 / Phase error: 24.63 / 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: 1.55→37.025 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: 5.7958 Å / Origin y: 19.5079 Å / Origin z: 23.0066 Å
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Refinement TLS group | Selection details: ALL |