+Open data
-Basic information
Entry | Database: PDB / ID: 5da5 | |||||||||
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Title | Crystal structure of Rhodospirillum rubrum Rru_A0973 | |||||||||
Components | Rru_A0973 | |||||||||
Keywords | OXIDOREDUCTASE / ferritin / iron / ferroxidase | |||||||||
Function / homology | Function and homology information encapsulin nanocompartment / ferroxidase / ferroxidase activity / iron ion transport / intracellular iron ion homeostasis / metal ion binding Similarity search - Function | |||||||||
Biological species | Rhodospirillum rubrum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.064 Å | |||||||||
Authors | He, D. / Vanden Hehier, S. / Georgiev, A. / Altenbach, K. / Tarrant, E. / Mackay, C.L. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J. | |||||||||
Funding support | China, United Kingdom, 2items
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Citation | Journal: Elife / Year: 2016 Title: Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments. Authors: He, D. / Hughes, S. / Vanden-Hehir, S. / Georgiev, A. / Altenbach, K. / Tarrant, E.J. / Mackay, C.L. / Waldron, K.J. / Clarke, D.J. / Marles-Wright, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5da5.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5da5.ent.gz | 868.7 KB | Display | PDB format |
PDBx/mmJSON format | 5da5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5da5 ftp://data.pdbj.org/pub/pdb/validation_reports/da/5da5 | HTTPS FTP |
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-Related structure data
Related structure data | 5l89C 5l8bC 5l8gC 3k6cS 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13347.675 Da / Num. of mol.: 30 / Fragment: UNP residues 1-96 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) / Gene: Rru_A0973 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2RVS1 #2: Chemical | ChemComp-FE / #3: Chemical | ChemComp-GOA / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % / Description: 200 um x 50 um rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1 - 2 ul protein mixed with 1 ul well solution over 1 ml well solution. 0.14 M calcium acetate 15 % (w/v) PEG3350 PH range: 7-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.7311 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7311 Å / Relative weight: 1 |
Reflection | Resolution: 2.064→49.63 Å / Num. all: 395746 / Num. obs: 395746 / % possible obs: 99.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.123 / Rsym value: 0.147 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.064→2.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.6 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3K6C Resolution: 2.064→49.627 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.064→49.627 Å
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Refine LS restraints |
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LS refinement shell |
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