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Open data
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Basic information
Entry | Database: PDB / ID: 1jdl | ||||||
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Title | Structure of cytochrome c2 from Rhodospirillum Centenum | ||||||
![]() | CYTOCHROME C2, ISO-2 | ||||||
![]() | ELECTRON TRANSPORT / ALPHA HELIX | ||||||
Function / homology | ![]() photosynthesis / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Camara-Artigas, A. / Williams, J.C. / Allen, J.P. | ||||||
![]() | ![]() Title: Structure of cytochrome c2 from Rhodospirillum centenum. Authors: Camara-Artigas, A. / Williams, J.C. / Allen, J.P. #1: ![]() Title: Interaction Between Cytochrome c2 and Reaction Centers from Purple Bacteria Authors: Wang, S. / Li, X. / Williams, J.C. / Allen, J.P. / Mathis, P. #2: ![]() Title: Relationship Between Rate and Free Energy Difference for Electron Transfer from Cytochrome c2 to the Reaction Center in Rhodobacter sphaeroides. Authors: Lin, X. / Williams, J.C. / Allen, J.P. / Mathis, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.1 KB | Display | ![]() |
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PDB format | ![]() | 25.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c2cS 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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Unit cell |
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Components
#1: Protein | Mass: 13052.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.139 Å3/Da / Density % sol: 42.54 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 6000, potassium phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 277 K | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||
Reflection | Resolution: 1.7→20 Å / Num. all: 13248 / Num. obs: 13248 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 16.9 % / Biso Wilson estimate: 21.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 2986 | ||||||||||||||||
Reflection shell | Resolution: 1.7→20 Å / Redundancy: 10 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 149 / Num. unique all: 1169 / % possible all: 88.4 | ||||||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 223519 / Rmerge(I) obs: 0.07 | ||||||||||||||||
Reflection shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 88.4 % / Num. unique obs: 1169 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2c2c Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 8.4 % / Rfactor obs: 0.192 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 25.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.289 / Rfactor obs: 0.249 |