+Open data
-Basic information
Entry | Database: PDB / ID: 1akw | |||||||||
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Title | G61L OXIDIZED FLAVODOXIN MUTANT | |||||||||
Components | FLAVODOXIN | |||||||||
Keywords | ELECTRON TRANSPORT / ELECTRON TRANSFER / FLAVOPROTEIN / FMN / FLAVODOXIN / MUTANT | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Mccarthy, A. / Walsh, M. / Higgins, T. | |||||||||
Citation | Journal: Biochemistry / Year: 1998 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: Journal: To Be Published Title: X-Ray Crystallographic Studies on the Flavin Binding Site of Flavodoxin from Desulfovibrio Vulgaris Authors: Mccarthy, A. #2: Journal: J.Mol.Biol. / Year: 1991 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: Journal: J.Biol.Chem. / Year: 1988 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: Journal: Fems Microbiol.Lett. / Year: 1988 Title: Cloning and Sequencing of the Gene Encoding Flavodoxin from Desulfovibrio Vulgaris Hildenborough Authors: Curley, G.P. / Voordouw, G. #5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1akw.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1akw.ent.gz | 30.3 KB | Display | PDB format |
PDBx/mmJSON format | 1akw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1akw ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1akw | HTTPS FTP |
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-Related structure data
-Links
-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: 15760.252 Da / Num. of mol.: 1 / Mutation: G61L Source method: isolated from a genetically manipulated source Details: OXIDIZED Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Description: SULFUR REDUCING BACTERIA / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00323 |
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#2: Chemical | ChemComp-FMN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.4 % | |||||||||||||||||||||||||
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. obs: 18715 / % possible obs: 99.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.46 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.72→1.75 Å / Redundancy: 2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 110226 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 96.4 % / Rmerge(I) obs: 0.337 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→40 Å / Cross valid method: R-FREE
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Displacement parameters | Biso mean: 25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 40 Å / Luzzati sigma a obs: 0.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→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: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.4 Å2 |