[English] 日本語
Yorodumi- PDB-2exv: Crystal structure of the F7A mutant of the cytochrome c551 from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2exv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the F7A mutant of the cytochrome c551 from Pseudomonas aeruginosa | ||||||
Components | Cytochrome c-551 | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome c / alpha helix / heme c | ||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Bonivento, D. / Di Matteo, A. / Borgia, A. / Travaglini-Allocatelli, C. / Brunori, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 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: Journal: J.Mol.Biol. / Year: 1982 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: Journal: J.Biol.Chem. / Year: 2000 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: Journal: J.Biol.Chem. / Year: 2005 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2exv.cif.gz | 46.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2exv.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 2exv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/2exv ftp://data.pdbj.org/pub/pdb/validation_reports/ex/2exv | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8628.796 Da / Num. of mol.: 2 / Mutation: F7A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: nirM / Production host: Escherichia coli (E. coli) / References: UniProt: P00099 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.335 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.155 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.86→1.908 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|