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Yorodumi- PDB-4ugl: Structure of Bacillus subtilis Nitric Oxide Synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ugl | ||||||
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Title | Structure of Bacillus subtilis Nitric Oxide Synthase in complex with N1-(3-(2-(6-Amino-4-methylpyridin-2-yl)ethyl)-5-fluorophenyl)-N1- cyclopropyl-N2-methylethane-1,2-diamine | ||||||
Components | NITRIC OXIDE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / 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: 1.82 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 | 4ugl.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ugl.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ugl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ugl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ugl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ugl_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 4ugl_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/4ugl ftp://data.pdbj.org/pub/pdb/validation_reports/ug/4ugl | HTTPS FTP |
-Related structure data
Related structure data | 4ug5C 4ug6C 4ug7C 4ug8C 4ug9C 4ugaC 4ugbC 4ugcC 4ugdC 4ugeC 4ugfC 4uggC 4ughC 4ugiC 4ugjC 4ugkC 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 , 6 types, 301 molecules
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-H4B / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-S90 / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | E25A, E26A, E316A INTRODUCED |
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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: 2.89 Å3/Da / Density % sol: 57.4 % Description: CC ONE HALF FOR FULL DATASET AT 0.999. CC ONE HALF FOR HIGH RESOLUTION SHELL AT 0.575. RMERGE FOR HIGH RESOLUTION SHELL AT 1.994 |
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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: BL11-1 / Wavelength: 0.97891 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→37.89 Å / Num. obs: 44089 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 30.34 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.82→1.86 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4D3T Resolution: 1.82→37.886 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.92 / 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: 1.82→37.886 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: 5.7194 Å / Origin y: 19.661 Å / Origin z: 23.0973 Å
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Refinement TLS group | Selection details: CHAIN A |