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Yorodumi- PDB-3qhc: Crystal structure of Symerythrin from Cyanophora paradoxa, reduce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qhc | ||||||
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Title | Crystal structure of Symerythrin from Cyanophora paradoxa, reduced with dithionite | ||||||
Components | Symerythrin | ||||||
Keywords | OXIDOREDUCTASE / four-helix bundle / rubrerythrin-like / carboxylate bridged-diiron / ferritin-like / ferritin-like superfamily | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyanophora paradoxa (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 | 3qhc.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qhc.ent.gz | 150.7 KB | Display | PDB format |
PDBx/mmJSON format | 3qhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qhc_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 3qhc_full_validation.pdf.gz | 451.9 KB | Display | |
Data in XML | 3qhc_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 3qhc_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qh/3qhc ftp://data.pdbj.org/pub/pdb/validation_reports/qh/3qhc | HTTPS FTP |
-Related 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: 19882.162 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanophora paradoxa (eukaryote) / Cellular location: Plastid; Cyanelle / Gene: ORF180 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48329 #2: Chemical | ChemComp-FE / #3: 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: 44.95 % |
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Crystal grow | Temperature: 279 K / Method: hanging drop / pH: 5.5 Details: PEG3350, NH4Cl, BisTris, dithionite, pH 5.5, 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: 0.976 Å |
Detector | Type: ADSC Q315R / Detector: CCD / Date: Sep 23, 2010 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30.6 Å / Num. all: 95243 / Num. obs: 95243 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.25→1.31 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 5.4 / Num. unique all: 13875 / Rsym value: 0.405 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→26.68 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.093 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.036 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 58.57 Å2 / Biso mean: 16.7486 Å2 / Biso min: 4.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→26.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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