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Open data
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Basic information
Entry | Database: PDB / ID: 3f6r | ||||||
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Title | Desulfovibrio desulfuricans (ATCC 29577) oxidized flavodoxin | ||||||
![]() | Flavodoxin | ||||||
![]() | ELECTRON TRANSPORT / flavodoxin-like fold / FMN binding / oxidized / Flavoprotein / FMN / Transport | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Guelker, M. / Shamoo, Y. | ||||||
![]() | ![]() Title: Pseudosymmetry, high copy number and twinning complicate the structure determination of Desulfovibrio desulfuricans (ATCC 29577) flavodoxin. Authors: Guelker, M. / Stagg, L. / Wittung-Stafshede, P. / Shamoo, 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 | ![]() | 130.7 KB | Display | ![]() |
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PDB format | ![]() | 101.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 29.5 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f6sC ![]() 1azlS 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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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15706.387 Da / Num. of mol.: 4 / Mutation: N79D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-FMN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 0.1M sodium citrate, 2.4M ammonium sulfate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2008 / Details: Rigaku Varimax HF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection twin | Operator: h,-k,-l / Fraction: 0.475 |
Reflection | Resolution: 1.97→37.53 Å / Num. all: 39723 / Num. obs: 29589 / % possible obs: 74.5 % / Observed criterion σ(I): 3 / Redundancy: 5.39 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 1.79 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3929 / % possible all: 14.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1AZL with side chains pruned to the last common atom Resolution: 2→37.53 Å / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 1.94 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.615 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2→37.53 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 98 %
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