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- PDB-1cmn: CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cmn | ||||||
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Title | CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND THEIR SER286 MUTANTS AT CRYOGENIC TEMPERATURE | ||||||
![]() | CYTOCHROME P450 | ||||||
![]() | OXIDOREDUCTASE / NITRIC OXIDE REDUCTASE / CYTOCHROME P450NOR / NO-LIGANDED / MUTAGENESIS(S286V) | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Park, S.-Y. / Shiro, Y. | ||||||
![]() | ![]() 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 | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 73.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cl6C ![]() 1cmjC ![]() 1romS C: citing same article ( S: Starting model for refinement |
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Similar 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: 44301.547 Da / Num. of mol.: 1 / Mutation: S286V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P23295, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-NO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 41 % Description: ROTATION AND TRANSLATION SEARCH IN THE X-PLOR PACKAGE | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 100MM-MES BUFFER AT PH 7.0 USING PEG4K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, sitting drop / Details: Park, S.Y., (1997) FEBS Lett. 412, 346. | ||||||||||||||||||||||||||||||
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: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1998 / Details: MIRROR/MONOCHROMATOR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 41933 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 6.16 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.224 / % possible all: 90.4 |
Reflection | *PLUS Num. measured all: 258529 |
Reflection shell | *PLUS % possible obs: 90.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ROM Resolution: 1.7→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 14.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.277 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.261 |