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- PDB-1xf6: High resolution crystal structure of phycoerythrin 545 from the m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1xf6 | ||||||
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Title | High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24 | ||||||
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![]() | PHOTOSYNTHESIS / phycoerythrin / light-harvesting protein / cryptophyte | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Doust, A.B. / Marai, C.N.J. / Harrop, S.J. / Wilk, K.E. / Curmi, P.M.G. / Scholes, G.D. | ||||||
![]() | ![]() Title: Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy Authors: Doust, A.B. / Marai, C.N.J. / Harrop, S.J. / Wilk, K.E. / Curmi, P.M.G. / Scholes, G.D. #1: ![]() Title: Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution Authors: Wilk, K.E. / Harrop, S.J. / Jankova, L. / Edler, D. / Keenan, G. / Sharples, F. / Hiller, R.G. / Curmi, P.M.G. #2: Journal: J.Biol.Chem. / Year: 1992 Title: Phycobilins of cryptophycean algae. Occurrence of dihydrobiliverdin and mesobiliverdin in cryptomonad biliproteins Authors: Wedemayer, G.J. / Kidd, D.G. / Wemmer, D.E. / Glazer, A.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.3 KB | Display | ![]() |
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PDB format | ![]() | 209.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1015.6 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 27.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xg0C ![]() 1qgwS S: Starting model for refinement C: citing same article ( |
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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
-Phycoerythrin alpha- ... , 2 types, 2 molecules AB
#1: Protein | Mass: 8135.157 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 7027.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 1 types, 2 molecules CD
#3: Protein | Mass: 18539.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 1075 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/DBV.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DBV.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/PEB.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-PEB / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.77 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→60.86 Å / Num. all: 905573 / Num. obs: 186884 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 5.6 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.033 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.1→1.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 8.4 / Rsym value: 0.137 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1QGW Resolution: 1.1→60.86 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.495 / SU ML: 0.011 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.022 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.253 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→60.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.114 Å / Total num. of bins used: 40
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