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Yorodumi- PDB-1i83: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i83 | ||||||
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Title | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH N1,N14-BIS((S-METHYL)ISOTHIOUREIDO)TETRADECANE (H4B FREE) | ||||||
Components | NITRIC OXIDE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / ALPHA-BETA FOLD | ||||||
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 Å | ||||||
Authors | Raman, C.S. / Li, H. / Martasek, P. / Babu, B.R. / Griffith, O.W. / Masters, B.S.S. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Implications for isoform-selective inhibitor design derived from the binding mode of bulky isothioureas to the heme domain of endothelial nitric-oxide synthase. Authors: Raman, C.S. / Li, H. / Martasek, P. / Babu, B.R. / Griffith, O.W. / Masters, B.S. / Poulos, T.L. #1: Journal: Cell(Cambridge,Mass.) / Year: 1998 Title: Crystal Structure of Constitutive Endothelial Nitric Oxide Synthase: A Paradigm for Pterin Function Involving a Novel Metal Center Authors: Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S.S. / Poulos, T.L. #2: Journal: Science / Year: 1998 Title: Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate Authors: Crane, B.R. / Arvai, A.S. / Ghosh, D.K. / Wu, C. / Getzoff, E.D. / Stuehr, D.J. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i83.cif.gz | 187.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i83.ent.gz | 154.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i83.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i83_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1i83_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1i83_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 1i83_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i83 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i83 | HTTPS FTP |
-Related 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: 49814.090 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell line: EPITHELIAL CELLS / Production host: Escherichia coli (E. coli) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 6 types, 508 molecules
#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.72 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG3350, cacodylate, MgSO4, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 280K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 Details: Raman, C.S., (1998) Cell (Cambridge,Mass.), 95, 939. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 61326 / % possible obs: 89.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 84.4 |
Reflection | *PLUS Num. measured all: 243479 |
Reflection shell | *PLUS % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→44.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2455508.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: RESIDUES 39 TO 66 OF MOLECULE A AND RESIDUES 39 TO 68 IN MOLECULE B ARE NOT VISIBLE IN THE ELECTRON DENSITY. RESIDUES 108-120 ARE DISORDERED, BUT THE TENTATIVE MODEL WAS INCLUDED IN THE REFINEMENT.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.6 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→44.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.382 / % reflection Rfree: 5.4 % / Rfactor Rwork: 0.368 |