+Open data
-Basic information
Entry | Database: PDB / ID: 1akq | ||||||
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Title | D95A OXIDIZED FLAVODOXIN MUTANT FROM D. 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: 1.9 Å | ||||||
Authors | Mccarthy, A. / Walsh, M. / Higgins, T. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystallographic investigation of the role of aspartate 95 in the modulation of the redox potentials of Desulfovibrio vulgaris flavodoxin. Authors: McCarthy, A.A. / Walsh, M.A. / Verma, C.S. / O'Connell, D.P. / Reinhold, M. / Yalloway, G.N. / D'Arcy, D. / Higgins, T.M. / Voordouw, G. / Mayhew, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1akq.cif.gz | 42.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1akq.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 1akq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1akq ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1akq | 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
#1: Protein | Mass: 15660.137 Da / Num. of mol.: 1 / Mutation: D95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Species: Desulfovibrio vulgaris / Strain: HILDENBOROUGH / Cellular location: CYTOPLASM / 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: 2.9 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN WAS CRYSTALLIZED FROM 60-70% A.S., 100MM TRIS-HCL, PH=7.0. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.5 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→10 Å / Num. obs: 17939 / % possible obs: 98 % / Redundancy: 2.8 % / Biso Wilson estimate: 19.25 Å2 / Rmerge(I) obs: 0.52 / Net I/σ(I): 16.68 |
Reflection shell | Resolution: 1.83→1.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.2 / % possible all: 67 |
Reflection | *PLUS Num. measured all: 70384 |
Reflection shell | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.298 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→10 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 19.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 / Rfactor Rfree: 0.2363 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |