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- PDB-6fsi: Crystal structure of semiquinone Flavodoxin 1 from Bacillus cereu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fsi | ||||||
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Title | Crystal structure of semiquinone Flavodoxin 1 from Bacillus cereus (1.32 A resolution) | ||||||
![]() | Flavodoxin | ||||||
![]() | ELECTRON TRANSPORT / flavodoxin / electron transfer / FMN | ||||||
Function / homology | ![]() oxidoreductase activity, acting on NAD(P)H / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gudim, I. / Lofstad, M. / Hersleth, H.-P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus. Authors: Gudim, I. / Lofstad, M. / van Beek, W. / 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 | ![]() | 115.7 KB | Display | ![]() |
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PDB format | ![]() | 90.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.2 KB | Display | ![]() |
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Full document | ![]() | 818 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 15.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fsgC ![]() 6ft1C ![]() 1wsbS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 16115.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BC_1376 / Plasmid: pET22b(+) / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-SO4 / |
#4: Sugar | ChemComp-GLC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 3.6 M ammonium sulfate and 0.1 M citric acid pH 4 (final pH 5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.6983 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→35.15 Å / Num. obs: 34618 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 6.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.32→1.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 13.6 / Num. unique obs: 1678 / CC1/2: 0.989 / Rpim(I) all: 0.046 / Rrim(I) all: 0.102 / % possible all: 99.4 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1WSB Resolution: 1.32→29.459 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 9.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 137.37 Å2 / Biso mean: 9.7963 Å2 / Biso min: 1.63 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.32→29.459 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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