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- PDB-1jay: Structure of Coenzyme F420H2:NADP+ Oxidoreductase (FNO) with its ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jay | ||||||
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Title | Structure of Coenzyme F420H2:NADP+ Oxidoreductase (FNO) with its substrates bound | ||||||
![]() | Coenzyme F420H2:NADP+ Oxidoreductase (FNO) | ||||||
![]() | STRUCTURAL GENOMICS / Rossmann fold | ||||||
Function / homology | ![]() 8-hydroxy-5-deazaflavin:NADPH oxidoreductase / : / 8-hydroxy-5-deazaflavin:NADPH oxidoreductase activity / ferric-chelate reductase (NADPH) activity / coenzyme F420 binding / cupric reductase (NADH) activity / copper ion import / NADPH regeneration / NADP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Warkentin, E. / Mamat, B. / Thauer, R. / Ermler, U. / Shima, S. | ||||||
![]() | ![]() Title: Structures of F420H2:NADP+ oxidoreductase with and without its substrates bound. Authors: Warkentin, E. / Mamat, B. / Sordel-Klippert, M. / Wicke, M. / Thauer, R.K. / Iwata, M. / Iwata, S. / Ermler, U. / Shima, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.8 KB | Display | ![]() |
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PDB format | ![]() | 82 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: 22894.318 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.58 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes pH7.5, 1.4 M tri-Na citrate, 1 mM F420, 1 mM NADP, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2000 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.957 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→40 Å / Num. all: 61974 / Num. obs: 61974 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.35 / Num. unique all: 3849 / % possible all: 72.4 |
Reflection | *PLUS Num. obs: 58452 |
Reflection shell | *PLUS Lowest resolution: 1.8 Å / % possible obs: 73.2 % / Rmerge(I) obs: 0.285 / Mean I/σ(I) obs: 2.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: FNO Resolution: 1.65→29.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1288595.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.62 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→29.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.291 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.273 |