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- PDB-3mg2: Crystal structure of the orange carotenoid protein Y44S mutant fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mg2 | |||||||||
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Title | Crystal structure of the orange carotenoid protein Y44S mutant from cyanobacteria synechocystis sp. PCC 6803 | |||||||||
![]() | Orange carotenoid protein | |||||||||
![]() | CAROTENOID BINDING PROTEIN / Echinone / Phycobilisome | |||||||||
Function / homology | ![]() light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Wilson, A. / Kinney, J. / Zwart, P.H. / Punginelli, C. / D'Haen, S. / Perreau, F. / Klein, M.G. / Kirilovsky, D. / Kerfeld, C.A. | |||||||||
![]() | ![]() Title: Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria. Authors: Wilson, A. / Kinney, J.N. / Zwart, P.H. / Punginelli, C. / D'Haene, S. / Perreau, F. / Klein, M.G. / Kirilovsky, D. / Kerfeld, C.A. #1: ![]() Title: The crystal structure of a cyanobacterial water-soluble carotenoid binding protein. Authors: Kerfeld, C.A. / Sawaya, M.R. / Brahmandam, V. / Cascio, D. / Ho, K.K. / Trevithick-Sutton, C.C. / Krogmann, D.W. / Yeates, T.O. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.2 KB | Display | ![]() |
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PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.5 KB | Display | ![]() |
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Full document | ![]() | 738.5 KB | Display | |
Data in XML | ![]() | 24.9 KB | Display | |
Data in CIF | ![]() | 33.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mg1C ![]() 3mg3C ![]() 3i1v 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | dimer |
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Components
#1: Protein | Mass: 35379.316 Da / Num. of mol.: 2 / Mutation: Y44S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | WATER MOLECULES 1001-1150 IN THE COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 12% PEG 4000, 100mM Sodium acetate, 2% Glycerol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2009 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.65→50 Å / Num. obs: 19757 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3I1V ![]() 3i1v Resolution: 2.653→37.542 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.98 / Phase error: 26.99 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.204 Å2 / ksol: 0.324 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.765 Å2
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Refinement step | Cycle: LAST / Resolution: 2.653→37.542 Å
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Refine LS restraints |
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LS refinement shell |
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