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Yorodumi- PDB-1d0c: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d0c | ||||||
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Title | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 3-BROMO-7-NITROINDAZOLE (H4B FREE) | ||||||
Components | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN | ||||||
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 / Resolution: 1.65 Å | ||||||
Authors | Raman, C.S. / Li, H. / Martasek, P. / Southan, G.J. / Masters, B.S.S. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structure of nitric oxide synthase bound to nitro indazole reveals a novel inactivation mechanism. Authors: Raman, C.S. / Li, H. / Martasek, P. / Southan, G. / 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. / 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. #3: Journal: Science / Year: 1997 Title: The Structure of Nitric Oxide Synthase Oxygenase Domain and Inhibitor Complexes Authors: Crane, B.R. / Arvai, A.S. / Gachhui, R. / Wu, C. / Ghosh, D.K. / 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 | 1d0c.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d0c.ent.gz | 155.3 KB | Display | PDB format |
PDBx/mmJSON format | 1d0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d0c_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1d0c_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1d0c_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 1d0c_validation.cif.gz | 60.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d0c ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d0c | 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: 49710.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell: ENDOTHELIAL CELLS / Production host: Escherichia coli (E. coli) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 670 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | ChemComp-INE / #6: Chemical | #7: Chemical | #8: 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: 2.38 Å3/Da / Density % sol: 48.38 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 4000, CACODYLATE, MAGNESSIUM ACETATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: ALS / Beamline: 5.0.2 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 30, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 116411 / Num. obs: 114549 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 3 % / Rmerge(I) obs: 0.586 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 398353 |
Reflection shell | *PLUS % possible obs: 99.1 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Resolution: 1.65→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.65→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.213 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |