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Yorodumi- PDB-5y5m: SFX structure of cytochrome P450nor: a complete dark data without... -
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-Basic information
Entry | Database: PDB / ID: 5y5m | ||||||
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Title | SFX structure of cytochrome P450nor: a complete dark data without pump laser (resting state) | ||||||
Components | NADP nitrous oxide-forming nitric oxide reductase | ||||||
Keywords | OXIDOREDUCTASE / metal-binding | ||||||
Function / homology | Function and homology information nitric oxide reductase [NAD(P)+, nitrous oxide-forming] / nitric oxide reductase (NAD(P)H) activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Model details | cytochrome P450nor in resting state, complete dark data | ||||||
Authors | Tosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. ...Tosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. / Sawai, H. / Takeda, H. / Mizohata, E. / Yamashita, A. / Kanematsu, Y. / Takano, Y. / Nango, E. / Tanaka, R. / Nureki, O. / Ikemoto, Y. / Murakami, H. / Owada, S. / Tono, K. / Yabashi, M. / Yamamoto, M. / Ago, H. / Iwata, S. / Sugimoto, H. / Shiro, Y. / Kubo, M. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate. Authors: Tosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. ...Authors: Tosha, T. / Nomura, T. / Nishida, T. / Saeki, N. / Okubayashi, K. / Yamagiwa, R. / Sugahara, M. / Nakane, T. / Yamashita, K. / Hirata, K. / Ueno, G. / Kimura, T. / Hisano, T. / Muramoto, K. / Sawai, H. / Takeda, H. / Mizohata, E. / Yamashita, A. / Kanematsu, Y. / Takano, Y. / Nango, E. / Tanaka, R. / Nureki, O. / Shoji, O. / Ikemoto, Y. / Murakami, H. / Owada, S. / Tono, K. / Yabashi, M. / Yamamoto, M. / Ago, H. / Iwata, S. / Sugimoto, H. / Shiro, Y. / Kubo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y5m.cif.gz | 182.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y5m.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 5y5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/5y5m ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y5m | HTTPS FTP |
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-Related structure data
Related structure data | 5y5fC 5y5gC 5y5hC 5y5iC 5y5jC 5y5kC 5y5lC 1cl6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1408089 / Data set type: diffraction image data |
Experimental dataset #2 | Data reference: 10.11577/1408090 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 44420.691 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: CYP55A1, CYP55 / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P23295, nitric oxide reductase [NAD(P)+, nitrous oxide-forming] #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8.5 Details: 34-38% PEG 10000, 0.1 M BIS-TRIS PROPANE 0.15 M Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.24 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Dec 6, 2016 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 47209 / % possible obs: 100 % / Redundancy: 307.5 % / Biso Wilson estimate: 42.3 Å2 / CC1/2: 0.991 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.1→2.12 Å / Redundancy: 213.3 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.541 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CL6 Resolution: 2.1→19.919 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.18 Å2 / Biso mean: 45.6859 Å2 / Biso min: 27.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→19.919 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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