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- PDB-1f25: CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f25 | ||||||
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Title | CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ASN MUTANTS OF CYTOCHROME P450NOR | ||||||
![]() | NITRIC OXIDE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / nitric oxide reductase / Cytochrome P450nor | ||||||
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. / Park, S.-Y. | ||||||
![]() | ![]() Title: Mutation effects of a conserved threonine (Thr243) of cytochrome P450nor on its structure and function. Authors: Obayashi, E. / Shimizu, H. / Park, S.Y. / Shoun, H. / Shiro, Y. #1: ![]() 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. #2: ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.6 KB | Display | ![]() |
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PDB format | ![]() | 152.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.1 KB | Display | ![]() |
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Full document | ![]() | 476.8 KB | Display | |
Data in XML | ![]() | 9.7 KB | Display | |
Data in CIF | ![]() | 17.8 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 44302.496 Da / Num. of mol.: 1 / Mutation: T243N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.07 % | |||||||||||||||||||||||||||||||||||||||||||||
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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 pH: 7.2 / Details: Shimizu, H., (2000) J. Inorg. Biochem., 81, 191. | |||||||||||||||||||||||||||||||||||||||||||||
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: Oct 5, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→10 Å / Num. all: 685047 / Num. obs: 76306 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 9 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.129 / Num. unique all: 11024 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 685047 |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
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Refinement | Resolution: 1.4→10 Å / σ(F): 0 / Stereochemistry target values: SHELX-97
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.142 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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