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Yorodumi- PDB-4d7i: Structure of Bacillus subtilis nitric oxide synthase I218V in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d7i | ||||||
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Title | Structure of Bacillus subtilis nitric oxide synthase I218V in complex with 6-(4-(((3-Fluorophenethyl)amino)methyl)phenyl)-4-methylpyridin-2- amine | ||||||
Components | NITRIC OXIDE SYNTHASE OXYGENASE | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE | ||||||
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 SUBSP. SUBTILIS STR. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Holden, J.K. / Poulos, T.L. | ||||||
Citation | Journal: Chem.Biol. / Year: 2015 Title: Nitric Oxide Synthase as a Target for Methicillin-Resistant Staphylococcus Aureus Authors: Holden, J.K. / Kang, S. / Beasley, F.C. / Cinelli, M.A. / Li, H. / Roy, S.G. / Dejam, D. / Edinger, A.L. / Nizet, 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 | 4d7i.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d7i.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 4d7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7i ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7i | HTTPS FTP |
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-Related structure data
Related structure data | 4d7hC 4d7jC 4d7oC 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: 41773.055 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168 (bacteria) 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, 226 molecules
#2: Chemical | ChemComp-HEM / |
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#3: Chemical | ChemComp-H4B / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-0GD / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | SURFACE ENTROPY MUTATIONS E25A, E26A AND E316A. MUTATION I218V 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: 2.82 Å3/Da / Density % sol: 56.43 % / Description: NONE |
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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: 8.2.2 / Wavelength: 0.9997 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 21, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9997 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→2.01 Å / Num. obs: 34480 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 27.56 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.96→2.01 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.5 / 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 ENRTY 4LWA Resolution: 1.96→48.944 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 27.48 / 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: 1.96→48.944 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: 5.6019 Å / Origin y: 19.8184 Å / Origin z: 22.3265 Å
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Refinement TLS group | Selection details: ALL |