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Yorodumi- PDB-2yxc: The H25M mutant of tetraheme cytochrome c3 from Desulfovibrio Vul... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yxc | ||||||
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Title | The H25M mutant of tetraheme cytochrome c3 from Desulfovibrio Vulgaris Miyazaki F | ||||||
Components | Cytochrome c3 | ||||||
Keywords | ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information anaerobic respiration / electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Higuchi, Y. / Komori, H. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Strategic roles of axial histidines in structure formation and redox regulation of tetraheme cytochrome c3. Authors: Takayama, Y. / Werbeck, N.D. / Komori, H. / Morita, K. / Ozawa, K. / Higuchi, Y. / Akutsu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yxc.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yxc.ent.gz | 29.8 KB | Display | PDB format |
PDBx/mmJSON format | 2yxc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/2yxc ftp://data.pdbj.org/pub/pdb/validation_reports/yx/2yxc | HTTPS FTP |
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-Related structure data
Related structure data | 2ewkC 1j0oS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 11551.331 Da / Num. of mol.: 1 / Mutation: H25M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris str. 'Miyazaki F' (bacteria) Species: Desulfovibrio vulgaris / Strain: Miyazaki F / Plasmid: pKF19k / Production host: Shewanella oneidensis (bacteria) / Strain (production host): TSP-C / References: UniProt: P00132 | ||
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#2: Chemical | ChemComp-HEM / #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: 2.61 Å3/Da / Density % sol: 52.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 / Details: pH 7.0, VAPOR DIFFUSION, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→12.23 Å / Num. obs: 18745 / Biso Wilson estimate: 14.8 Å2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J0O Resolution: 1.5→12.23 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 780091.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.6859 Å2 / ksol: 0.380368 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→12.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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