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Yorodumi- PDB-1f24: CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ALA MUTANTS OF CYTOCHROM... -
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-Basic information
Entry | Database: PDB / ID: 1f24 | ||||||
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Title | CRYSTAL STRUCTURE OF NO COMPLEX OF THR243ALA MUTANTS OF CYTOCHROME P450NOR | ||||||
Components | NITRIC OXIDE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / nitric oxide reductase / Cytochrome P450nor | ||||||
Function / homology | Function and homology information 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 | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å | ||||||
Authors | Shimizu, H. / Park, S.-Y. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2000 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: Journal: J.Biol.Chem. / Year: 2000 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: Journal: Nat.Struct.Biol. / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f24.cif.gz | 198.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f24.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/1f24 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/1f24 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44259.473 Da / Num. of mol.: 1 / Mutation: T243A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Plasmid: PRSET-C / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: P23295, nitric-oxide reductase |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.98 % | |||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.6 |
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: 696775 / Num. obs: 76100 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.129 / Num. unique all: 10999 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 696775 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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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: 0.139 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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