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Yorodumi- PDB-4cx0: Structure of bovine endothelial nitric oxide synthase Y477A mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cx0 | ||||||
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Title | Structure of bovine endothelial nitric oxide synthase Y477A mutant heme domain in complex with 6-((((3S, 5R)-5-(((6-AMINO-4- METHYLPYRIDIN-2-YL)METHOXY)METHYL)PYRROLIDIN-3-YL)OXY)METHYL)-4- METHYLPYRIDIN-2-AMINE | ||||||
Components | NITRIC OXIDE SYNTHASE, ENDOTHELIAL | ||||||
Keywords | 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 / OTHER / Resolution: 2.2 Å | ||||||
Authors | Li, H. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Mobility of a Conserved Tyrosine Residue Controls Isoform-Dependent Enzyme-Inhibitor Interactions in Nitric Oxide Synthases. Authors: Li, H. / Jamal, J. / Delker, S.L. / Plaza, C. / Ji, H. / Jing, Q. / Huang, H. / Kang, S. / 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 | 4cx0.cif.gz | 339.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cx0.ent.gz | 286.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cx0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cx0_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4cx0_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4cx0_validation.xml.gz | 36 KB | Display | |
Data in CIF | 4cx0_validation.cif.gz | 51.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/4cx0 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/4cx0 | HTTPS FTP |
-Related structure data
Related structure data | 4cwvC 4cwwC 4cwxC 4cwyC 4cwzC 4cx1C 4cx2C 4cx3C 4cx4C 4cx5C 4cx6C 4cx7C C: citing same article (ref.) |
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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: 49634.918 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 40-482 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 440 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE 100 IS FOUND AS AN ARG IN STRUCTURE BUT IS A CYS IN DATABASE |
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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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE |
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Crystal grow | pH: 6 Details: 20-22% PEG3350, 0.1M CACODYLATE PH 6.0, 150-200 MM MG ACETATE, 5 MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2012 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 50206 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 32.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / % possible all: 97.9 |
-Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.2→38.68 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.95 / SU B: 9.126 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. RESIDUES 110 TO 120 IN BOTH CHAIN A AND CHAIN B ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.058 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→38.68 Å
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Refine LS restraints |
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