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Yorodumi- PDB-1xg0: High resolution crystal structure of phycoerythrin 545 from the m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xg0 | ||||||
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Title | High resolution crystal structure of phycoerythrin 545 from the marine cryptophyte rhodomonas CS24 | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / PHYCOERYTHRIN / LIGHT-HARVESTING PROTEIN / CRYPTOPHYTE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhodomonas sp. CS24 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.97 Å | ||||||
Authors | Doust, A.B. / Marai, C.N.J. / Harrop, S.J. / Wilk, K.E. / Curmi, P.M.G. / Scholes, G.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 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: Journal: Proc.Natl.Acad.Sci.Usa / Year: 1999 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xg0.cif.gz | 259.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xg0.ent.gz | 206.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xg0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xg0 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xg0 | HTTPS FTP |
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-Related structure data
Related structure data | 1xf6C 1qgwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The Biological assembly is alpha1 aplha2 beta beta hetrodimer. |
-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) Rhodomonas sp. CS24 (eukaryote) / Strain: CS 24 / References: UniProt: Q00433 |
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#2: Protein | Mass: 7027.146 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodomonas sp. CS24 (eukaryote) / Strain: CS 24 / References: UniProt: P30943 |
-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) Rhodomonas sp. CS24 (eukaryote) / Strain: CS 24 / References: UniProt: P27198 |
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-Non-polymers , 5 types, 1063 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.88 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 19, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.966→60.86 Å / Num. all: 270473 / Num. obs: 249226 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 5.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 0.966→1.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.55 / % possible all: 82.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QGW Resolution: 0.97→60.86 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.455 / SU ML: 0.011 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.017 / ESU R Free: 0.019 / 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: 0.97→60.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.966→0.978 Å / Total num. of bins used: 40
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