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Yorodumi- PDB-1ed4: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ed4 | ||||||
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Title | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH IPITU (H4B FREE) | ||||||
Components | NITRIC OXIDE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE / HEME PROTEIN / 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 synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / 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 synthase activity / nitric oxide mediated signal transduction / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / mitochondrion organization / negative regulation of blood pressure / nitric oxide biosynthetic process / response to hormone / caveola / blood coagulation / FMN binding / flavin adenine dinucleotide binding / NADP binding / response to lipopolysaccharide / cytoskeleton / calmodulin binding / heme binding / Golgi apparatus / metal ion binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å | ||||||
Authors | Raman, C.S. / Li, H. / Martasek, P. / Kral, V. / Masters, B.S.S. / Poulos, T.L. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2000 Title: Mapping the active site polarity in structures of endothelial nitric oxide synthase heme domain complexed with isothioureas. Authors: Li, H. / Raman, C.S. / Martasek, P. / Kral, V. / 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 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 | 1ed4.cif.gz | 197 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ed4.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ed4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1ed4 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1ed4 | HTTPS FTP |
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-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 / Fragment: HEME DOMAIN (RESIDUES 39-482) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Cell: ENDOTHELIAL / Production host: Escherichia coli (E. coli) / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 7 types, 666 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-ZN / | #4: Chemical | #5: Chemical | ChemComp-IPU / #6: Chemical | #7: Chemical | ChemComp-GOL / #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: 2.44 Å3/Da / Density % sol: 49.51 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 4000, cacodylate, magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 280K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
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 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 5, 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: 1.86→50 Å / Num. obs: 78017 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.435 / % possible all: 89.4 |
Reflection | *PLUS Num. measured all: 283041 |
Reflection shell | *PLUS % possible obs: 89.4 % |
-Processing
Software |
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Refinement | Resolution: 1.86→36.73 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1946110.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: 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: 57.14 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.86→36.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.93 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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