+Open data
-Basic information
Entry | Database: PDB / ID: 3brp | ||||||
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Title | Crystal Structure of C-Phycocyanin from Galdieria sulphuraria | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / PHOTOSYSTEM II / LIGHT HARVESTING PROTEINS / RED ALGAE / THERMOSTABILITY / Bile pigment / Chloroplast / Chromophore / Electron transport / Membrane / Phycobilisome / Plastid / Thylakoid / Transport / Methylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Galdieria sulphuraria (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Fromme, R. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of C-Phycocyanin from Galdieria sulphuraria at 1.85 A Authors: Fromme, R. / Thangaraj, B. / Vanselow, C. / Fromme, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3brp.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3brp.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 3brp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3brp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3brp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3brp_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 3brp_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/3brp ftp://data.pdbj.org/pub/pdb/validation_reports/br/3brp | HTTPS FTP |
-Related structure data
Related structure data | 1ktpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | THE DODECAMER IN REMARK 350 REPRESENTS A HEXAMER OF HETERODIMER |
-Components
#1: Protein | Mass: 17520.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: P00306 | ||||
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#2: Protein | Mass: 18254.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: P00311 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | AUTHOR STATES THAT THE CONFLICTS WITH UNP DATABASE ARE DUE TO DIFFERENT SPECIES. THE SEQUENCE IN ...AUTHOR STATES THAT THE CONFLICTS WITH UNP DATABASE ARE DUE TO DIFFERENT SPECIES. THE SEQUENCE IN UNP ENTRIES ARE ACTURALLY FROM CYANIDIUM CALDARIUM, NOT FROM GALDIERIA SULPHURARI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 9.5% PEG 2000,0.1M HEPES, 0.1M MGCl2, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 30304 / Num. obs: 30145 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.516 / Rsym value: 0.538 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KTP Resolution: 1.85→10 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.247 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.185 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.896 Å / Total num. of bins used: 20
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