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- PDB-2ib5: Structural characterization of a blue chromoprotein and its yello... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ib5 | |||||||||
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Title | Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus | |||||||||
![]() | Chromo protein | |||||||||
![]() | LUMINESCENT PROTEIN / beta barrel / alpha helix / chromoprotein / chromophore / blue / GFP-like protein | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chan, M.C.Y. / Bosanac, I. / Ikura, M. | |||||||||
![]() | ![]() Title: Structural Characterization of a Blue Chromoprotein and Its Yellow Mutant from the Sea Anemone Cnidopus Japonicus Authors: Chan, M.C.Y. / Karasawa, S. / Mizuno, H. / Bosanac, I. / Ho, D. / Prive, G.G. / Miyawaki, A. / Ikura, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 393.8 KB | Display | ![]() |
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PDB format | ![]() | 322.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.3 KB | Display | ![]() |
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Full document | ![]() | 553.7 KB | Display | |
Data in XML | ![]() | 88.7 KB | Display | |
Data in CIF | ![]() | 117.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 | The biological assembly is a octomer generated from the tetramer in the asymmetric unit. |
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Components
#1: Protein | Mass: 26842.227 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | Sequence details | RESIDUES GLN 63, TYR 64 AND GLY 65 ARE MODIFIED TO FORM A CHROMOPHORE (CRQ 65) IN ALL CHAINS. ...RESIDUES GLN 63, TYR 64 AND GLY 65 ARE MODIFIED TO FORM A CHROMOPHOR | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M NaH2PO4, 20mM Tris-HCl, 150mM NaCl, 20% PEG3350, 20% glycerol, 2mM TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 9, 2004 Details: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator #2 double crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 335346 / Num. obs: 335346 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 52.7 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 5.1 / Num. unique all: 16336 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 19.5 Å2 | |||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.05
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