+Open data
-Basic information
Entry | Database: PDB / ID: 1azl | ||||||
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Title | G61V FLAVODOXIN MUTANT FROM DESULFOVIBRIO VULGARIS | ||||||
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: 1.8 Å | ||||||
Authors | Walsh, M.A. / Mccarthy, A. / O'Farrell, P.A. / Voordouw, G. / Higgins, T. / Mayhew, S.G. | ||||||
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: 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. #2: 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. #3: 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. #4: 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 | 1azl.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1azl.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 1azl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1azl_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 1azl_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 1azl_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1azl_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/1azl ftp://data.pdbj.org/pub/pdb/validation_reports/az/1azl | HTTPS FTP |
-Related structure data
-Links
-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.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Organ: SEED / Plasmid: PDK6 / 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: 2.6 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: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: CCP4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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