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- PDB-2exv: Crystal structure of the F7A mutant of the cytochrome c551 from P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2exv | ||||||
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Title | Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa | ||||||
![]() | Cytochrome c-551 | ||||||
![]() | ELECTRON TRANSPORT / cytochrome c / alpha helix / heme c | ||||||
Function / homology | ![]() periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bonivento, D. / Di Matteo, A. / Borgia, A. / Travaglini-Allocatelli, C. / Brunori, M. | ||||||
![]() | ![]() Title: Unveiling a Hidden Folding Intermediate in c-Type Cytochromes by Protein Engineering Authors: Borgia, A. / Bonivento, D. / Travaglini-Allocatelli, C. / Di Matteo, A. / Brunori, M. #1: ![]() Title: Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 A resolution and comparison of the two redox forms. Authors: Matsuura, Y. / Takano, T. / Dickerson, R.E. #2: ![]() Title: Selected mutations in a mesophilic cytochrome c confer the stability of a thermophilic counterpart. Authors: Hasegawa, J. / Uchiyama, S. / Tanimoto, Y. / Mizutani, M. / Kobayashi, Y. / Sambongi, Y. / Igarashi, Y. #3: ![]() Title: An obligatory intermediate in the folding pathway of cytochrome c552 from Hydrogenobacter thermophilus. Authors: Travaglini-Allocatelli, C. / Gianni, S. / Dubey, V.K. / Borgia, A. / Di Matteo, A. / Bonivento, D. / Bren, K.L. / Brunori, 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 | ![]() | 46.3 KB | Display | ![]() |
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PDB format | ![]() | 37.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8628.796 Da / Num. of mol.: 2 / Mutation: F7A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 26-30% PEG 4K, zinc acetate 0.2 M, sodium acetate 0.1 M, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 14, 2005 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→30 Å / Num. obs: 13460 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.86→1.93 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.665 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.908 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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