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Open data
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Basic information
Entry | Database: PDB / ID: 1akr | ||||||
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Title | G61A OXIDIZED FLAVODOXIN MUTANT | ||||||
![]() | FLAVODOXIN | ||||||
![]() | ELECTRON TRANSPORT / ELECTRON TRANSFER / FLAVOPROTEIN / FMN / FLAVODOXIN / MUTANT | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mccarthy, A. / Walsh, M. / Higgins, T. | ||||||
![]() | ![]() Title: Modulation of the redox potentials of FMN in Desulfovibrio vulgaris flavodoxin: thermodynamic properties and crystal structures of glycine-61 mutants. Authors: O'Farrell, P.A. / Walsh, M.A. / McCarthy, A.A. / Higgins, T.M. / Voordouw, G. / Mayhew, S.G. #1: ![]() Title: X-Ray Crystallographic Studies on the Flavin Binding Site of Flavodoxin from Desulfovibrio Vulgaris Authors: Mccarthy, A. #2: ![]() Title: Comparison of the Crystal Structures of a Flavodoxin in its Three Oxidation States at Cryogenic Temperatures Authors: Watt, W. / Tulinsky, A. / Swenson, R.P. / Watenpaugh, K.D. #3: ![]() Title: Cloning,Nucleotide Sequence,and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough) Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P. #4: ![]() Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough Authors: Curley, G.P. / Voordouw, G. #5: ![]() Title: Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstrom Resolution:Resolution of the Phase Ambiguity by Anomalous Scattering Authors: Watenpaugh, K.D. / Sieker, L.C. / Jensen, L.H. / Legall, J. / Dubourdieu, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.5 KB | Display | ![]() |
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PDB format | ![]() | 30.5 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 15718.172 Da / Num. of mol.: 1 / Mutation: G61A Source method: isolated from a genetically manipulated source Details: OXIDIZED Source: (gene. exp.) ![]() Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Description: SULFUR REDUCING BACTERIA / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 52 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: 60-70% AMMONIUM SULFATE, 100MM TRIS-HCL, pH 7.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→40 Å / Num. obs: 24403 / % possible obs: 98.9 % / Biso Wilson estimate: 19.72 Å2 / Rmerge(I) obs: 0.36 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.56→1.58 Å / Redundancy: 2 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 126829 / Rmerge(I) obs: 0.036 |
Reflection shell | *PLUS % possible obs: 87.6 % / Rmerge(I) obs: 0.341 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 25.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 40 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→40 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor obs: 0.184 / Rfactor Rfree: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.03 |