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- PDB-1kib: cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kib | |||||||||
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Title | cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in the form of an oblate shell | |||||||||
![]() | cytochrome c6 | |||||||||
![]() | ELECTRON TRANSPORT / cytochrome oligomer | |||||||||
Function / homology | ![]() plasma membrane-derived thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kerfeld, C.A. / Sawaya, M.R. / Krogmann, D. / Yeates, T.O. | |||||||||
![]() | ![]() Title: Structure of cytochrome c6 from Arthrospira maxima: an assembly of 24 subunits in a nearly symmetric shell. Authors: Kerfeld, C.A. / Sawaya, M.R. / Krogmann, D.W. / Yeates, T.O. #1: ![]() Title: Structures of Cytochrome c-549 and Cytochrome c6 from the Cyanobacterium Arthrospira maxima Authors: Sawaya, M.R. / Krogmann, D.W. / Serag, A. / Ho, K.K. / Yeates, T.O. / Kerfeld, C.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.5 KB | Display | ![]() |
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PDB format | ![]() | 119.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 24.6 KB | Display | |
Data in CIF | ![]() | 34.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f1fS S: Starting model for refinement |
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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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Unit cell |
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Components
#1: Protein | Mass: 9246.372 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-HEC / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.19 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.1M Tris pH 7.8, 2.4M ammonium sulfate, 5% methylpentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 27, 1995 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. all: 13268 / Num. obs: 13268 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.15 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 3.5→3.62 Å / Redundancy: 0.391 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 1352 / % possible all: 95.5 |
Reflection | *PLUS % possible obs: 91 % / Rmerge(I) obs: 0.15 |
Reflection shell | *PLUS % possible obs: 95.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.391 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1f1f Resolution: 3.5→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 41.3 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.2051 / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.202 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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