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Yorodumi- PDB-1dm6: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dm6 | ||||||
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Title | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH N-(4-CHLOROPHENYL)-N'-HYDROXYGUANIDINE (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 / Resolution: 1.95 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.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, A. #3: Journal: Biochemistry / Year: 1999 Title: Efficient Formation of Nitric Oxide from Selective Oxidation of N-Aryl N'- Hydroxyguanidines by Inducible Nitric Oxide Synthase Authors: Renodon-Corniere, A. / Boucher, J.-L. / Dijols, S. / Stuehr, D.J. / Mansuy, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dm6.cif.gz | 193.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dm6.ent.gz | 151.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dm6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dm6_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1dm6_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1dm6_validation.xml.gz | 38.9 KB | Display | |
Data in CIF | 1dm6_validation.cif.gz | 55.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm6 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm6 | 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 / Fragment: HEME DOMAIN 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 , 6 types, 529 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: Chemical | ChemComp-PH3 / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATED ...ZN ION SITS RIGHT ON THE NCS 2-FOLD THAT DEFINES THE DIMER INTERFACE AND IS COORDINATE |
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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: 2.41 Å3/Da / Density % sol: 49.03 % | ||||||||||||||||||||||||||||||||||||||||||
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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 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 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 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: 1.95→50 Å / Num. all: 71066 / Num. obs: 63487 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.779 / % possible all: 89.7 |
Reflection | *PLUS Num. measured all: 174140 |
Reflection shell | *PLUS % possible obs: 89.7 % / Mean I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Resolution: 1.95→28.2 Å / Rfactor Rfree error: 0.005 / 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: 52.9516 Å2 / ksol: 0.36575 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→28.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 28.2 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.22 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 38.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.382 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.38 |