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Yorodumi- PDB-3sid: Crystal structure of oxidized Symerythrin from Cyanophora paradox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sid | ||||||
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Title | Crystal structure of oxidized Symerythrin from Cyanophora paradoxa, azide adduct at 50% occupancy | ||||||
Components | Symerythrin | ||||||
Keywords | OXIDOREDUCTASE / Ferritin-like superfamily | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyanophora paradoxa (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Cooley, R.B. / Arp, D.J. / Karplus, P.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Symerythrin structures at atomic resolution and the origins of rubrerythrins and the ferritin-like superfamily. Authors: Cooley, R.B. / Arp, D.J. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sid.cif.gz | 184 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sid.ent.gz | 146.5 KB | Display | PDB format |
PDBx/mmJSON format | 3sid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sid_validation.pdf.gz | 437.9 KB | Display | wwPDB validaton report |
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Full document | 3sid_full_validation.pdf.gz | 444.1 KB | Display | |
Data in XML | 3sid_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3sid_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/3sid ftp://data.pdbj.org/pub/pdb/validation_reports/si/3sid | HTTPS FTP |
-Related structure data
Related structure data | 3qhcC 3qhbS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 20013.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanophora paradoxa (eukaryote) / Gene: Cyanelle ORF180 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48329 #2: Chemical | ChemComp-FE / #3: Chemical | #4: 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: 2.25 Å3/Da / Density % sol: 45.39 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 3350, 0.1M BisTris, 0.35M NH4Cl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9765 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2011 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30.74 Å / Num. all: 68857 / Num. obs: 68857 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Biso Wilson estimate: 13.96 Å2 / Rsym value: 0.074 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 12 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 5.6 / Num. unique all: 10086 / Rsym value: 0.441 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QHB Resolution: 1.4→30.74 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.629 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R Free: 0.052 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.676 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→30.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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