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- PDB-8brk: Room temperature crystal structure of cytochrome c' from Thermus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8brk | ||||||
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Title | Room temperature crystal structure of cytochrome c' from Thermus thermophilus | ||||||
![]() | Probable cytochrome | ||||||
![]() | ELECTRON TRANSPORT / Heme protein / diatomic gas binding protein / electron transfer | ||||||
Function / homology | Cytochrome P460 / Cytochrome P460 superfamily / Cytochrome P460 / HEME C / Probable cytochrome![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fujii, S. / Hough, M.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi. Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.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 | ![]() | 44.7 KB | Display | ![]() |
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PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 830.7 KB | Display | ![]() |
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Full document | ![]() | 831.9 KB | Display | |
Data in XML | ![]() | 8.5 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zckC ![]() 8a9dC ![]() 8ar6C ![]() 8ar9C ![]() 8brlC ![]() 8cifC ![]() 7eadS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 14942.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES pH 7, 0.2 M sodium chloride, 20% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Apr 13, 2022 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→35.14 Å / Num. obs: 12429 / % possible obs: 93.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 15.38 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.076 / Rrim(I) all: 0.17 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.75→1.78 Å / Rmerge(I) obs: 1.171 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 490 / CC1/2: 0.4 / Rpim(I) all: 0.74 / Rrim(I) all: 1.398 / % possible all: 74.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EAD Resolution: 1.75→35.14 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.523 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / 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: 23.947 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→35.14 Å
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Refine LS restraints |
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