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- PDB-4cdy: Spectroscopically-validated structure of cytochrome c prime from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4cdy | |||||||||
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Title | Spectroscopically-validated structure of cytochrome c prime from Alcaligenes xylosoxidans, reduced by X-ray irradiation at 160K | |||||||||
![]() | CYTOCHROME C' | |||||||||
![]() | ELECTRON TRANSPORT / RESONANCE RAMAN / VALIDATION / GAS SENSOR / LIGAND DISCRIMINATION / FERRIC / HAEM / HEME / RADIOLYSIS | |||||||||
Function / homology | ![]() electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kekilli, D. / Dworkowski, F. / Antonyuk, S. / Hough, M.A. | |||||||||
![]() | ![]() Title: Fingerprinting Redox and Ligand States in Haemprotein Crystal Structures Using Resonance Raman Spectroscopy. Authors: Kekilli, D. / Dworkowski, F.S. / Pompidor, G. / Fuchs, M.R. / Andrew, C.R. / Antonyuk, S. / Strange, R.W. / Eady, R.R. / Hasnain, S.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 | ![]() | 41.3 KB | Display | ![]() |
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PDB format | ![]() | 27.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.3 KB | Display | ![]() |
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Full document | ![]() | 790.3 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cdaC ![]() 4cdvC ![]() 4cipC ![]() 4cjgC ![]() 4cjoC ![]() 2yliS C: citing same article ( 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: 13631.442 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 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.2 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: AMMONIUM SULFATE, HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→45 Å / Num. obs: 15687 / % possible obs: 98.6 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / % possible all: 79.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2YLI Resolution: 1.77→45.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.521 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 34.666 Å2
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Refinement step | Cycle: LAST / Resolution: 1.77→45.03 Å
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Refine LS restraints |
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