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Yorodumi- PDB-5g6b: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g6b | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with two molecules of 7-((3-Fluorophenethylamino)ethyl)quinolin-2-amine | ||||||
Components | NITRIC OXIDE SYNTHASE OXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / INHIBITOR | ||||||
Function / homology | Function and homology information nitric-oxide synthase (flavodoxin) / nitric-oxide synthase activity / nitric oxide biosynthetic process / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | BACILLUS SUBTILIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å | ||||||
Authors | Holden, J.K. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g6b.cif.gz | 177.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g6b.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 5g6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g6b_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5g6b_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5g6b_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 5g6b_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g6/5g6b ftp://data.pdbj.org/pub/pdb/validation_reports/g6/5g6b | HTTPS FTP |
-Related structure data
Related structure data | 5g65C 5g66C 5g67C 5g68C 5g69C 5g6aC 5g6cC 5g6dC 5g6eC 5g6fC 5g6gC 5g6hC 5g6iC 5g6jC 5g6kC 5g6lC 5g6mC 5g6nC 5g6oC 5g6pC 5g6qC 4lwaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) BACILLUS SUBTILIS (bacteria) / Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O34453, EC: 1.14.13.165 |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | SURFACE ENTROPY MUTATIONS E25A, E26A AND E316A |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.5 % Description: CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.790. DATA SET HAD STRONG ANISOTROPY AND WAS FURTHER SCALED USING THE DIFFRACTION ANISOTROPY SERVER. |
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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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 25, 2015 / 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: 1.8→37.6 Å / Num. obs: 44728 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 19.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4LWA Resolution: 1.801→37.597 Å / SU ML: 0.14 / σ(F): 1.35 / Phase error: 20.12 / Stereochemistry target values: ML Details: MODEL WAS REFINED AGAINST REFLECTIONS 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: 1.801→37.597 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: 5.6158 Å / Origin y: 19.5632 Å / Origin z: 22.5386 Å
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Refinement TLS group | Selection details: ALL |