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Yorodumi- PDB-4uge: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uge | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with 4-methyl-6-((3-(piperidin-4-ylmethoxy)phenoxy)methyl)pyridin-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: 2.14 Å | ||||||
Authors | Holden, J.K. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uge.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uge.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 4uge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/4uge ftp://data.pdbj.org/pub/pdb/validation_reports/ug/4uge | HTTPS FTP |
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-Related structure data
Related structure data | 4ug5C 4ug6C 4ug7C 4ug8C 4ug9C 4ugaC 4ugbC 4ugcC 4ugdC 4ugfC 4uggC 4ughC 4ugiC 4ugjC 4ugkC 4uglC 4ugmC 4ugnC 4ugoC 4ugpC 4ugqC 4ugrC 4ugsC 4ugtC 4uguC 4ugvC 4ugwC 4ugxC 4ugyC 4d3tS 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 / Plasmid: PET28A / 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, 164 molecules
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-H4B / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-Q15 / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.1 % Description: CC ONE HALF FOR FULL DATA SET AT 0.9991. CC ONE HALF FOR HIGH RESOLUTION DATA SET AT 0.584 |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.999999 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999999 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→34.22 Å / Num. obs: 27187 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.14→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D3T Resolution: 2.14→34.219 Å / SU ML: 0.18 / σ(F): 1.36 / Phase error: 22.09 / 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: 2.14→34.219 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: 5.6648 Å / Origin y: 19.7088 Å / Origin z: 22.8614 Å
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Refinement TLS group | Selection details: ALL |