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- PDB-1jfc: X-ray structure of nitric oxide reductase (cytochrome P450nor) in... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jfc | ||||||
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Title | X-ray structure of nitric oxide reductase (cytochrome P450nor) in the ferrous CO state at atomic resolution | ||||||
![]() | nitric-oxide reductase Cytochrome P450 55A1 | ||||||
![]() | OXIDOREDUCTASE / nitric oxide reductase / Cytochrome P450nor / atomic resolution / carbon monoxide / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | ![]() nitric oxide reductase [NAD(P)+, nitrous oxide-forming] / nitric oxide reductase (NAD(P)H) activity / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shimizu, H. / Adachi, S. / Park, S.Y. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution. Authors: Shimizu, H. / Park, S.Y. / Shiro, Y. / Adachi, S. #1: ![]() Title: Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum Authors: Park, S.Y. / Shimizu, H. / Adachi, S. / Nakagawa, A. / Tanaka, I. / Nakahara, K. / Shoun, H. / Obayashi, E. / Nakamura, H. / Iizuka, T. / Shiro, Y. #2: ![]() Title: Proton Delivery in No Reduction by Fungal Nitric-Oxide Reductase. Cryogenic Crystallography, Spectroscopy, and Kinetics of Ferric-No Complexes of Wild- Type and Mutant Enzymes Authors: Shimizu, H. / Obayashi, E. / Gomi, Y. / Arakawa, H. / Park, S.Y. / Nakamura, H. / Adachi, S. / Shoun, H. / Shiro, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 292.6 KB | Display | ![]() |
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PDB format | ![]() | 240 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 550.5 KB | Display | ![]() |
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Full document | ![]() | 558.5 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44521.793 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-CMO / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.38 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG3350, MES, Glycerol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop / Details: used microseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Monochromator: Si(111) flat / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1→100 Å / Num. all: 2238315 / Num. obs: 175256 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.05→1.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 2.8 / Num. unique all: 28478 / % possible all: 91.3 |
Reflection | *PLUS Highest resolution: 1.05 Å / Lowest resolution: 100 Å / Num. measured all: 2238315 |
Reflection shell | *PLUS % possible obs: 91.3 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.05→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 38397 / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.117 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |