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Yorodumi- PDB-5aur: Hydrogenobacter thermophilus cytochrome c552 dimer formed by doma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aur | |||||||||
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Title | Hydrogenobacter thermophilus cytochrome c552 dimer formed by domain swapping at N-terminal region | |||||||||
Components | Cytochrome c-552 | |||||||||
Keywords | ELECTRON TRANSPORT / Electron transfer | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Hydrogenobacter thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.26 Å | |||||||||
Authors | Ren, C. / Nagao, S. / Yamanaka, M. / Kamikubo, H. / Komori, H. / Shomura, Y. / Higuchi, Y. / Hirota, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Mol Biosyst / Year: 2015 Title: Oligomerization enhancement and two domain swapping mode detection for thermostable cytochrome c552via the elongation of the major hinge loop. Authors: Ren, C. / Nagao, S. / Yamanaka, M. / Komori, H. / Shomura, Y. / Higuchi, Y. / Hirota, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5aur.cif.gz | 158.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5aur.ent.gz | 125.3 KB | Display | PDB format |
PDBx/mmJSON format | 5aur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/5aur ftp://data.pdbj.org/pub/pdb/validation_reports/au/5aur | HTTPS FTP |
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-Related structure data
Related structure data | 5ausC 1ynrS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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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-Components
#1: Protein | Mass: 8757.169 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6) (bacteria) Strain: DSM 6534 / IAM 12695 / TK-6 / Gene: HTH_0988, Hydth_0984 / Production host: Escherichia coli (E. coli) / Strain (production host): JCB387 / References: UniProt: P15452 #2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200 mM potassium iodide, 15% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→50 Å / Num. obs: 74408 / % possible obs: 94.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.26→1.29 Å / Redundancy: 2 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.2 / % possible all: 93.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YNR Resolution: 1.26→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.906 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.829 Å2
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Refinement step | Cycle: 1 / Resolution: 1.26→50 Å
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Refine LS restraints |
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