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- PDB-8c16: Crystal structure of asymmetric ferredoxin/flavodoxin NADP+ oxido... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8c16 | |||||||||
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Title | Crystal structure of asymmetric ferredoxin/flavodoxin NADP+ oxidoreductase 2 (FNR2) H326V mutant from Bacillus cereus | |||||||||
![]() | Ferredoxin--NADP reductase | |||||||||
![]() | OXIDOREDUCTASE / FERREDOXIN/FLAVODOXIN REDUCTASE / ELECTRON TRANSFER / FAD / FLAVOPROTEIN / MUTANT | |||||||||
Function / homology | ![]() ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rugtveit, A.K. / Hammerstad, M. / Hersleth, H.-P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction. Authors: Hammerstad, M. / Rugtveit, A.K. / Dahlen, S. / Andersen, H.K. / Hersleth, H.P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 318.1 KB | Display | ![]() |
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PDB format | ![]() | 207.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 814.8 KB | Display | ![]() |
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Full document | ![]() | 835.3 KB | Display | |
Data in XML | ![]() | 28.9 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8avhC ![]() 8aviC ![]() 8c3mC ![]() 6gasS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 6 - 318 / Label seq-ID: 6 - 318
NCS oper:
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Components
#1: Protein | Mass: 36754.094 Da / Num. of mol.: 4 / Mutation: H326V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 24 mg/mL protein (1:1) 10% w/v PEG 4000, 20% v/v glycerol, 0.02 M sodium l-glutamate, 0.02 M dl-alanine, 0.02 M glycine, 0.02 M dl-lysine HCl, 0.02 M dl-serine, 0.1 M bicine/Trizma base pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 18, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976254 Å / Relative weight: 1 |
Reflection | Resolution: 4.2→75.48 Å / Num. obs: 11894 / % possible obs: 95.8 % / Redundancy: 4 % / Biso Wilson estimate: 157.81 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.093 / Rrim(I) all: 0.202 / Χ2: 1.01 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 4.2→4.7 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3352 / CC1/2: 0.552 / Rpim(I) all: 0.499 / Rrim(I) all: 1.092 / Χ2: 1.02 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6GAS Resolution: 4.2→75.48 Å / SU ML: 0.6695 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.2221 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 185.98 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.2→75.48 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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