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Yorodumi- PDB-1p6n: Bovine endothelial NOS heme domain with L-N(omega)-nitroarginine-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p6n | ||||||
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Title | Bovine endothelial NOS heme domain with L-N(omega)-nitroarginine-(4R)-amino-L-proline amide bound | ||||||
Components | Nitric-oxide synthase, endothelial | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide synthase / heme-enzyme | ||||||
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: 2.5 Å | ||||||
Authors | Flinspach, M.L. / Li, H. / Jamal, J. / Yang, W. / Huang, H. / Hah, J.-M. / Gomez-Vidal, J.A. / Litzinger, E.A. / Silverman, R.B. / Poulos, T.L. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase. Authors: Flinspach, M.L. / Li, H. / Jamal, J. / Yang, W. / Huang, H. / Hah, J.M. / Gomez-Vidal, J.A. / Litzinger, E.A. / Silverman, R.B. / 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: Biochemistry / Year: 2002 Title: The novel binding mode of N-alkyl-N'-hydroxyguanidine to neuronal nitric oxide synthase provides mechanistic insights into NO biosynthesis Authors: Li, H. / Shimizu, H. / Flinspach, M. / Jamal, J. / Yang, W. / Xian, M. / Cai, T. / Wen, E.Z. / Jia, Q. / Wang, P.G. / Poulos, T.L. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR STATED THAT STRUCTURAL DATA CLEARLY INDICATED THAT RESIDUE 100 IS ARG RATHER THAN CYS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p6n.cif.gz | 187.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p6n.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 1p6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p6n_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1p6n_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1p6n_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 1p6n_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p6n ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p6n | HTTPS FTP |
-Related structure data
Related structure data | 1p6hC 1p6iC 1p6jC 1p6kC 1p6lC 1p6mC 1q2oC 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: 46983.207 Da / Num. of mol.: 2 / Fragment: NOS HEME DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: endothelial nitric oxide synthase / Plasmid: pPICZ / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: P29473, nitric-oxide synthase (NADPH) |
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-Non-polymers , 8 types, 300 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-ZN / | #8: Chemical | #9: 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: 2.55 Å3/Da / Density % sol: 51.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: PEG 3350, MgOAc, Na Cacodylate, TCEP, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 280K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 5 ℃ / Method: vapor diffusion, sitting drop / Details: Li, H., (2002) Biochemistry, 41, 13868. / PH range low: 6 / PH range high: 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 27, 2001 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 36082 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.72 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.665 / % possible all: 98 |
Reflection | *PLUS Num. obs: 34984 / % possible obs: 99.7 % / Num. measured all: 128881 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→42.55 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.1463 Å2 / ksol: 0.342913 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→42.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.54 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 33894 / % reflection Rfree: 5 % / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.219 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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