+Open data
-Basic information
Entry | Database: PDB / ID: 1c7f | ||||||
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Title | D95E 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | McCarthy, A. / Walsh, M. / Higgins, T. / D'Arcy, D. | ||||||
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 | 1c7f.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c7f.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 1c7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c7f_validation.pdf.gz | 1018.6 KB | Display | wwPDB validaton report |
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Full document | 1c7f_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1c7f_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 1c7f_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c7f ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c7f | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.40173, -0.91575, -0.0048), Vector: |
-Components
#1: Protein | Mass: 15718.172 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (bacteria) / Strain: TG2 / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): TG2 / References: UniProt: P00323 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 59.8 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 70-70% A.S. 210MM TRIS-HCL PH=6.5, 200MM SODIUM ACETATE | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8.5 / 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 15532 / % possible obs: 94.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 23.18 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.8 / % possible all: 91.9 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 19635 / Num. measured all: 52226 |
Reflection shell | *PLUS % possible obs: 91.9 % / Rmerge(I) obs: 0.224 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.8 Å / SU B: 3.75 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.16
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Displacement parameters | Biso mean: 26.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor obs: 0.1797 / Rfactor Rfree: 0.2379 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |