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Yorodumi- PDB-1dmi: BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dmi | ||||||
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Title | BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 6S-H4B | ||||||
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: 2 Å | ||||||
Authors | Raman, C.S. / Li, H. / Martasek, P. / Kotsonis, P. / Pfleiderer, W. / Schmidt, H.H.H.W. / Masters, B.S.S. / Poulos, T.L. | ||||||
Citation | Journal: To be Published Title: Crystal Structures of Bovine Endothelial Nitric Oxide Synthase Heme Domain Complexed with the Pterin Analogues Authors: Raman, C.S. / Li, H. / Martasek, P. / Kotsonis, P. / Pfleiderer, W. / Schmidt, H.H.H.W. / Southan, G.J. / Masters, B.S.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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dmi.cif.gz | 192.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dmi.ent.gz | 149.7 KB | Display | PDB format |
PDBx/mmJSON format | 1dmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dmi_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1dmi_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1dmi_validation.xml.gz | 38.7 KB | Display | |
Data in CIF | 1dmi_validation.cif.gz | 54 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dmi ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dmi | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 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 , 8 types, 403 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | #9: 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: 2.46 Å3/Da / Density % sol: 50.02 % |
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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 |
-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: Dec 12, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 63795 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.587 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Resolution: 2→32.59 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2575244.45 / 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: 57.51 Å2 / ksol: 0.364 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
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Xplor file |
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