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Yorodumi- PDB-2zbo: Crystal structure of low-redox-potential cytochrom c6 from brown ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zbo | ||||||
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Title | Crystal structure of low-redox-potential cytochrom c6 from brown alga Hizikia fusiformis at 1.6 A resolution | ||||||
Components | Cytochrome c6 | ||||||
Keywords | ELECTRON TRANSPORT / cytochrome c6 / redox potential / brown alga / Heme / Iron / Metal-binding / Transit peptide | ||||||
Function / homology | Function and homology information chloroplast thylakoid lumen / electron transfer activity / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Hizikia fusiformis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Akazaki, H. / Kawai, F. / Chida, H. / Matsumoto, Y. / Sirasaki, I. / Nakade, H. / Hirayama, M. / Hosikawa, K. / Suruga, K. / Satoh, T. ...Akazaki, H. / Kawai, F. / Chida, H. / Matsumoto, Y. / Sirasaki, I. / Nakade, H. / Hirayama, M. / Hosikawa, K. / Suruga, K. / Satoh, T. / Yamada, S. / Unzai, S. / Hakamata, W. / Nishio, T. / Park, S.-Y. / Oku, T. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2008 Title: Cloning, expression and purification of cytochrome c(6) from the brown alga Hizikia fusiformis and complete X-ray diffraction analysis of the structure Authors: Akazaki, H. / Kawai, F. / Chida, H. / Matsumoto, Y. / Hirayama, M. / Hoshikawa, K. / Unzai, S. / Hakamata, W. / Nishio, T. / Park, S.-Y. / Oku, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zbo.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zbo.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/2zbo ftp://data.pdbj.org/pub/pdb/validation_reports/zb/2zbo | HTTPS FTP |
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-Related structure data
Related structure data | 1gdvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 9155.002 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hizikia fusiformis (eukaryote) / Strain: brown alga / Gene: petJ / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76FN8 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-SO4 / #4: 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: 3.79 Å3/Da / Density % sol: 67.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 0.1M CAPS pH 10.5, 0.2M Li2SO4, 2.2M AmSO4, 3% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 107513 |
Reflection shell | Resolution: 1.6→1.66 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GDV Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.315 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.315 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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