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Yorodumi- PDB-3rqo: Structure of the endothelial nitric oxide synthase heme domain in... -
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-Basic information
Entry | Database: PDB / ID: 3rqo | ||||||
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Title | Structure of the endothelial nitric oxide synthase heme domain in complex with 6-(((3R,4R)-4-(2-((1S,2R/1R,2S)-2-(3-Clorophenyl)cyclopropylamino)ethoxy)pyrrolidin-3-yl)methyl)-4-methylpyridin-2-amine | ||||||
Components | Nitric oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / oxidoreductase / enzyme-inhibitor complex / OXIDOREDUCTASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure ...cellular response to laminar fluid shear stress / positive regulation of guanylate cyclase activity / negative regulation of leukocyte cell-cell adhesion / nitric-oxide synthase (NADPH) / nitric oxide mediated signal transduction / nitric-oxide synthase activity / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / nitric oxide biosynthetic process / negative regulation of blood pressure / response to hormone / mitochondrion organization / caveola / blood coagulation / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to lipopolysaccharide / calmodulin binding / cytoskeleton / heme binding / Golgi apparatus / nucleus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.08 Å | ||||||
Authors | Li, H. / Delker, S.L. / Poulos, T.L. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2013 Title: Cyclopropyl- and methyl-containing inhibitors of neuronal nitric oxide synthase. Authors: Li, H. / Xue, F. / Kraus, J.M. / Ji, H. / Labby, K.J. / Mataka, J. / Delker, S.L. / Martasek, P. / Roman, L.J. / Poulos, T.L. / Silverman, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rqo.cif.gz | 346.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rqo.ent.gz | 279.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rqo_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3rqo_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3rqo_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 3rqo_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/3rqo ftp://data.pdbj.org/pub/pdb/validation_reports/rq/3rqo | HTTPS FTP |
-Related structure data
Related structure data | 3rqjC 3rqkC 3rqlC 3rqmC 3rqnC 3rqpC 1nseS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 49623.027 Da / Num. of mol.: 2 / Fragment: UNP residues 40-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: NOS3 / Plasmid: pCWori / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 8 types, 416 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ZN / | #9: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE CHEMICAL (X2D) USED FOR THE CRYSTAL SOAKING WAS A MIXTURE OF TWO DIASTEREOMERS AS INDICATED BY ...THE CHEMICAL (X2D) USED FOR THE CRYSTAL SOAKING WAS A MIXTURE OF TWO DIASTEREOM |
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Sequence details | C100R CONFLICT IN UNP ENTRY P29473 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 12-14% PEG3350, 0.1M Cacodylate, 0.2M magnesium acetate, 5mM TCEP, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2011 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→50 Å / Num. obs: 59039 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.08→2.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.66 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1NSE Resolution: 2.08→35.11 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / SU B: 10.228 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R Free: 0.166 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.204 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→35.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.08→2.135 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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