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Open data
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Basic information
Entry | Database: PDB / ID: 1azl | ||||||
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Title | G61V FLAVODOXIN MUTANT FROM DESULFOVIBRIO VULGARIS | ||||||
![]() | FLAVODOXIN | ||||||
![]() | ELECTRON TRANSPORT / ELECTRON TRANSFER / FLAVOPROTEIN / FMN / FLAVODOXIN / MUTANT | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Walsh, M.A. / Mccarthy, A. / O'Farrell, P.A. / Voordouw, G. / Higgins, T. / Mayhew, S.G. | ||||||
![]() | ![]() 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: 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. #2: ![]() Title: Cloning,Nucleotide Sequence,and Expression of the Flavodoxin Gene from Desulfovibrio Vulgaris (Hildenborough) Authors: Krey, G.D. / Vanin, E.F. / Swenson, R.P. #3: ![]() Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough Authors: Curley, G.P. / Voordouw, G. #4: ![]() 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 | ![]() | 45.2 KB | Display | ![]() |
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PDB format | ![]() | 30.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.5 KB | Display | ![]() |
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Full document | ![]() | 460.5 KB | Display | |
Data in XML | ![]() | 5.9 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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
#1: Protein | Mass: 15746.225 Da / Num. of mol.: 1 / Mutation: G61V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Organ: SEED / Plasmid: PDK6 / 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: 2.6 Å3/Da / Density % sol: 53 % Description: MODEL USED WAS UNSUBMITTED REFINED FLAVODOXIN FROM DESULFOVIBRIO FLAVODOXIN, IDENTICAL TO PDB ENTRY 2FX2 | |||||||||||||||||||||||||
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Crystal grow | Method: macroseeding / pH: 7 Details: PROTEIN SEED CRYSTALS WERE OBTAINED FROM 60-70% AMMONIUM SULFATE, 10MM TRIS PH 7.0, 1-2% ACETONE. MACROSEEDS WERE TRANSFERRED TO THE ABOVE SOLUTION WITH NO ACETONE PRESENT., macroseeding | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1992 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 12653 / % possible obs: 89.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.49 / % possible all: 79.9 |
Reflection | *PLUS Num. obs: 19560 / % possible obs: 98 % / Num. measured all: 87934 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 82.6 % / Rmerge(I) obs: 0.441 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: RECOMBINANT FLAVODOXIN Resolution: 1.8→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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